@sjcrh/proteinpaint-client 2.204.0 → 2.206.0
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.
- package/dist/2dmaf-5OYM4MXA.js +1367 -0
- package/dist/AggMatrixInput-4VTI4Y6E.js +277 -0
- package/dist/AggregateMatrix-K7SGNO63.js +41 -0
- package/dist/AppHeader-WU6TO2OZ.js +830 -0
- package/dist/BoxPlot-OW7U3XTF.js +1211 -0
- package/dist/CorrelationVolcano-B3JTTZHF.js +614 -0
- package/dist/Cuminc-AJEXWRU2.js +1219 -0
- package/dist/DE-2J7DSRPC.js +89 -0
- package/dist/DE-2J7DSRPC.js.map +7 -0
- package/dist/DEinput-I7JWNOSD.js +499 -0
- package/dist/DEinput-I7JWNOSD.js.map +7 -0
- package/dist/DM-NQ46YPGF.js +90 -0
- package/dist/DM-NQ46YPGF.js.map +7 -0
- package/dist/DifferentialAnalysis-BFCQBX5J.js +237 -0
- package/dist/Disco-ZJLVQRTC.js +3389 -0
- package/dist/Disco.UI-AEDACXW2.js +243 -0
- package/dist/DmrPlot-QMRXAOM3.js +637 -0
- package/dist/GB-MFU2UJ22.js +1391 -0
- package/dist/GSEA-E3NHU22A.js +851 -0
- package/dist/GeneExpInput-MIUNSOPY.js +362 -0
- package/dist/Geomap-HAJG3STN.js +84 -0
- package/dist/HicApp-ECFFIRWI.js +2245 -0
- package/dist/IDCViewer-TNSD3U2V.js +10812 -0
- package/dist/NumBinaryEditor-CNBGZ6WY.js +279 -0
- package/dist/NumBinaryEditor.unit.spec-SKFDALF3.js +312 -0
- package/dist/NumContEditor-7ID2U7JL.js +105 -0
- package/dist/NumContEditor.unit.spec-XHSQSAWK.js +164 -0
- package/dist/NumCustomBinEditor-PAIPRJPO.js +33 -0
- package/dist/NumCustomBinEditor.unit.spec-QYVZMMHV.js +397 -0
- package/dist/NumDiscreteEditor-K2NZZQTH.js +170 -0
- package/dist/NumDiscreteEditor.unit.spec-3CG5VEQL.js +233 -0
- package/dist/NumRegularBinEditor-EOVZ22TP.js +33 -0
- package/dist/NumRegularBinEditor.unit.spec-FHTVH5FH.js +278 -0
- package/dist/NumSplineEditor-N3REMJUC.js +210 -0
- package/dist/NumSplineEditor.unit.spec-DZCP35GL.js +224 -0
- package/dist/NumericDensity-42MWVI2S.js +33 -0
- package/dist/NumericDensity.unit.spec-T2HHSQON.js +418 -0
- package/dist/NumericHandler-5XU3SSPD.js +34 -0
- package/dist/NumericHandler.unit.spec-3F23KSAQ.js +214 -0
- package/dist/ProteomeInput-UN2BUNRO.js +388 -0
- package/dist/Regression-HWLJENA5.js +1416 -0
- package/dist/RunChart2-YO55WE4M.js +749 -0
- package/dist/SC-LEDJ4DQR.js +1107 -0
- package/dist/Violin-E6PDJZ2B.js +1082 -0
- package/dist/Volcano-XJTBWYUK.js +1649 -0
- package/dist/Volcano-XJTBWYUK.js.map +7 -0
- package/dist/Wsi-S675CYTW.js +431 -0
- package/dist/adSandbox-ZJQ5ZW2T.js +33 -0
- package/dist/animatedBubbleChart-LRUS7W36.js +547 -0
- package/dist/app-7Q3QIBU4.js +32 -0
- package/dist/app-PKSI4MV5.js +42 -0
- package/dist/app.js +17 -17
- package/dist/bam-X5JH5ZT7.js +876 -0
- package/dist/barchart-UT6J4L2N.js +42 -0
- package/dist/barchart2-ZG5QJO3C.js +309 -0
- package/dist/block-TC466NGW.js +6249 -0
- package/dist/block.init-CIBNSYAC.js +33 -0
- package/dist/block.mds.expressionrank-EY5PCQCK.js +354 -0
- package/dist/block.mds.geneboxplot-R6AOMHO5.js +823 -0
- package/dist/block.mds.junction-JMV6FNYC.js +1539 -0
- package/dist/block.mds.svcnv-IHTV3QYG.js +6796 -0
- package/dist/block.svg-NTFLVQAQ.js +159 -0
- package/dist/block.tk.aicheck-FYPL32Y4.js +278 -0
- package/dist/block.tk.ase-FWCB6VBO.js +360 -0
- package/dist/block.tk.bam-Q5UFUABN.js +1901 -0
- package/dist/block.tk.bedgraphdot-KBI3GFDM.js +379 -0
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- package/dist/block.tk.hicstraw-MQBH3YAJ.js +818 -0
- package/dist/block.tk.junction-EBTVXLJH.js +2358 -0
- package/dist/block.tk.junction.textmatrixui-ETYLCP2O.js +194 -0
- package/dist/block.tk.ld-NLB6L6WQ.js +94 -0
- package/dist/block.tk.menu-PJLCOXVJ.js +1024 -0
- package/dist/block.tk.pgv-JOIQVWL2.js +938 -0
- package/dist/brainImaging-SPRC3QFB.js +515 -0
- package/dist/brainRegions-LGQGRWG7.js +217 -0
- package/dist/brainRegions-LGQGRWG7.js.map +7 -0
- package/dist/bubbleHeatmap-CFTZ5RXH.js +378 -0
- package/dist/cellTypeBubbleHeatmap-DXPLFT5U.js +278 -0
- package/dist/chunk-2BQ572SL.js +102 -0
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- package/dist/chunk-2POQWEK6.js +134 -0
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- package/dist/chunk-WTAPOH2W.js.map +7 -0
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- package/dist/cohort-FZNMFWOX.js +70 -0
- package/dist/condition-AJJLFCBQ.js +327 -0
- package/dist/controls-SZOLV37V.js +34 -0
- package/dist/controls.config-CVP75WFA.js +34 -0
- package/dist/correlation-UFJFQHQ3.js +95 -0
- package/dist/customdata.inputui-HOVA4A6O.js +284 -0
- package/dist/dataDownload-VTUG4IOK.js +329 -0
- package/dist/databrowser.ui-O5S4Y4EK.js +425 -0
- package/dist/dictionary-L2UNNNP7.js +113 -0
- package/dist/dnaMethylation-B4SWZI4O.js +33 -0
- package/dist/dnaMethylation.integration.spec-ANJAMNYJ.js +198 -0
- package/dist/dofetch-F5XSHQIS.js +48 -0
- package/dist/e2pca-66ARIMKL.js +344 -0
- package/dist/ep-OFGJYVUY.js +1249 -0
- package/dist/expclust.gdc.spec-22RXQTTP.js +302 -0
- package/dist/facet-GVZQ3RPN.js +519 -0
- package/dist/gb-HEPGVYEK.js +81 -0
- package/dist/geneExpClustering-3NU2U422.js +244 -0
- package/dist/geneExpression-FXQ4L2J2.js +310 -0
- package/dist/geneExpression-XYVYJJA5.js +33 -0
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- package/dist/geneORA-5M2JSDMF.js +273 -0
- package/dist/geneRanking-TP3R3CS3.js +548 -0
- package/dist/geneVariant-232EYUFJ.js +36 -0
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- package/dist/geneset-N42FIVA6.js +203 -0
- package/dist/genomeBrowser.spec-5HKQKLRU.js +276 -0
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- /package/dist/{samplelst-7NGH3SUM.js.map → samplelst-ZD63EYO7.js.map} +0 -0
- /package/dist/{samplematrix-SNAR6IBB.js.map → samplematrix-ZZ3DVELU.js.map} +0 -0
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- /package/dist/{singlecell-SO3B5KJ7.js.map → singlecell-22OG6HNI.js.map} +0 -0
- /package/dist/{singlecell-CDUQ6MTO.js.map → singlecell-7TBALI2S.js.map} +0 -0
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- /package/dist/{sunburst-266MA7E2.js.map → sunburst-G7DGATWP.js.map} +0 -0
- /package/dist/{survival-CAZCIY2N.js.map → survival-MKNABJPU.js.map} +0 -0
- /package/dist/{svgraph-OFUESREM.js.map → svgraph-VB7JWWR5.js.map} +0 -0
- /package/dist/{svmr-PVH42MY4.js.map → svmr-VLQIO2U5.js.map} +0 -0
- /package/dist/{table-C2SICFZV.js.map → table-EAXMDWOY.js.map} +0 -0
- /package/dist/{termCollection-TGYDI7NP.js.map → termCollection-5LG7ICQY.js.map} +0 -0
- /package/dist/{termCollection-H4RL5WJG.js.map → termCollection-SB6MWLFK.js.map} +0 -0
- /package/dist/{termCollection.unit.spec-JSALS7GL.js.map → termCollection.unit.spec-H5ITGTR3.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection-YJVDNV4I.js.map → termCollectionFractionSelection-2XZSTDCQ.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection.unit.spec-4GM7P4ZW.js.map → termCollectionFractionSelection.unit.spec-BIO7V6KA.js.map} +0 -0
- /package/dist/{tk-RZCPSHJG.js.map → tk-TRWYZLQ2.js.map} +0 -0
- /package/dist/{tk-SNTRA5CC.js.map → tk-VZI5HNSX.js.map} +0 -0
- /package/dist/{tp.ui-2W4K3XH6.js.map → tp.ui-J5SNNAT3.js.map} +0 -0
- /package/dist/{tvs.dt-GIPVC3R6.js.map → tvs.dt-6YHFJPER.js.map} +0 -0
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- /package/dist/{tvs.dtitd-TM6UROSH.js.map → tvs.dtitd-VSYMR3OD.js.map} +0 -0
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- /package/dist/{tvs.dtsv-Y5QEJPYG.js.map → tvs.dtsv-S743GBB5.js.map} +0 -0
- /package/dist/{tvs.numeric-3UXW4JHJ.js.map → tvs.numeric-22AHXO5K.js.map} +0 -0
- /package/dist/{tvs.samplelst-MLAFPFER.js.map → tvs.samplelst-XAJO4EM6.js.map} +0 -0
- /package/dist/{tvs.termCollection-ZQQDKESH.js.map → tvs.termCollection-QOVJGAUC.js.map} +0 -0
- /package/dist/{vocabulary-JRUZPHMG.js.map → vocabulary-6EADTHP3.js.map} +0 -0
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import {
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getEmptyCell,
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maySetEmptyCell,
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setCellProps
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} from "./chunk-OVPEMVXT.js";
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import {
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TermTypeGroups
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} from "./chunk-IZUYLFOX.js";
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import {
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__export
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} from "./chunk-HS5PO5ZQ.js";
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// plots/matrix/matrix.serieses.js
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var matrix_serieses_exports = {};
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__export(matrix_serieses_exports, {
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getSerieses: () => getSerieses
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});
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function getSerieses(data) {
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const s = this.settings.matrix;
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const serieses = [];
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const { colw, dx, dy, xMin, xMax } = this.dimensions;
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const dvt = this.config.divideBy || {};
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const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
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const legendGroups = {};
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this.colorScaleByTermId = {};
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for (const t of this.termOrder) {
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const $id = t.tw.$id;
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const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
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const isDivideByTerm = termid === divideByTermId;
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const emptyGridCells = [];
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const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
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const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
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const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
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const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
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const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
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const series = {
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t,
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tw: t.tw,
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cells: [],
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y,
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hoverY0,
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hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
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};
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for (const so of this.unfilteredSampleOrder) {
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const { totalIndex, grpIndex, row } = so;
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series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
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const anno = row[$id];
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const cellTemplate = {
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s: so,
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sample: row.sample,
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tw: t.tw,
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term: t.tw.term,
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termid,
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$id,
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totalIndex,
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grpIndex,
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row,
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t,
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seriesY: y
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};
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if (!anno) {
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if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
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const cell = getEmptyCell(cellTemplate, s, this.dimensions);
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series.cells.push(cell);
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}
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continue;
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}
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const key = anno.key;
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const values = anno.filteredValues || anno.values || [anno.value];
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const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
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const height = !s.transpose ? s.rowh / numRects : colw;
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const width = !s.transpose ? colw : colw / values.length;
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const siblingCells = [];
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if (!anno || !anno.renderedValues?.length) {
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if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
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const cell = getEmptyCell(cellTemplate, s, this.dimensions);
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series.cells.push(cell);
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}
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continue;
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}
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for (const [i, value] of values.entries()) {
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const cell = Object.assign({ key, siblingCells }, cellTemplate);
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cell.valueIndex = i;
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let legend;
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if (typeof t.tw.setCellProps == "function") {
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legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
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} else {
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const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
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legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
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}
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if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
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if (legend) {
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for (const l of [legendGroups, so.grp.legendGroups]) {
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if (!l) continue;
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if (!l[legend.group]) {
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l[legend.group] = {
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ref: legend.ref,
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values: {},
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order: legend.order,
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$id,
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origin: legend.entry.origin
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};
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if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
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}
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const lg = l[legend.group];
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if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
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const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
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if (!lg.values[legendK]) {
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lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
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if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
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}
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if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
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if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
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if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
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} else lg.values[legendK].samples.add(row.sample);
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if (isDivideByTerm) {
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lg.values[legend.value].isExcluded = so.grp.isExcluded;
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}
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}
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}
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if (!so.grp.isExcluded) {
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if (anno.renderedValues.includes(value)) series.cells.push(cell);
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siblingCells.push(cell);
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}
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}
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if (s.showGrid == "rect" && !so.grp.isExcluded) {
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const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions, this);
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if (cell) emptyGridCells.push(cell);
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}
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}
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if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
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if (series.cells.length) serieses.push(series);
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}
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addAllHiddenLegendGroups(legendGroups, this);
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this.legendData = this.getLegendData(legendGroups, data.refs, this);
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for (const grp of this.sampleGroups) {
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grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
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}
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return serieses;
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}
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function addAllHiddenLegendGroups(legendGroups, self) {
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for (const valueFilter of self.config.legendValueFilter.lst) {
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if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
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legendGroups[valueFilter.tvs.term.$id] = {
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ref: {},
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values: {},
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$id: valueFilter.tvs.term.$id
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};
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} else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
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legendGroups[valueFilter.legendGrpName] = {
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ref: {},
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values: {},
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dt: [valueFilter.tvs.values[0].dt],
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origin: valueFilter.tvs.values[0].origin
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};
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156
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} else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
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legendGroups[valueFilter.tvs.term.$id] = {
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ref: {},
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159
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values: {},
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$id: valueFilter.tvs.term.$id
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};
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}
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}
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}
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export {
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getSerieses,
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168
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matrix_serieses_exports
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169
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};
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//# sourceMappingURL=chunk-SWO6DZTG.js.map
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@@ -0,0 +1,387 @@
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import {
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addBrushes,
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3
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addNewBrush
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4
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} from "./chunk-A7OWXDYA.js";
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import {
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6
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niceNumLabels,
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7
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violinRenderer
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8
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} from "./chunk-7X6NF7NI.js";
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import {
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convertUnits,
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11
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+
getValueConversionFactor
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12
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} from "./chunk-W5J3LTYS.js";
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13
|
+
import {
|
|
14
|
+
NumericRangeInput
|
|
15
|
+
} from "./chunk-FXQXCOII.js";
|
|
16
|
+
import {
|
|
17
|
+
select_default
|
|
18
|
+
} from "./chunk-I6Y4O3RR.js";
|
|
19
|
+
|
|
20
|
+
// filter/tvs.numeric.js
|
|
21
|
+
var handler = {
|
|
22
|
+
type: "numeric",
|
|
23
|
+
term_name_gen,
|
|
24
|
+
get_pill_label,
|
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25
|
+
getSelectRemovePos,
|
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26
|
+
fillMenu,
|
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27
|
+
setTvsDefaults
|
|
28
|
+
};
|
|
29
|
+
function term_name_gen(d) {
|
|
30
|
+
const name = d.term.name;
|
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31
|
+
return name.length < 26 ? name : '<label title="' + name + '">' + name.substring(0, 24) + "...</label>";
|
|
32
|
+
}
|
|
33
|
+
function get_pill_label(tvs) {
|
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34
|
+
if (tvs.ranges.length == 1) {
|
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35
|
+
const v = tvs.ranges[0];
|
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36
|
+
if ("value" in v) {
|
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37
|
+
if (v.label) return { txt: v.label };
|
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38
|
+
if (tvs.term.values && tvs.term.values[v.value] && tvs.term.values[v.value].label)
|
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39
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+
return { txt: tvs.term.values[v.value].label };
|
|
40
|
+
console.error(`key "${v.value}" not found in values{} of ${tvs.term.name}`);
|
|
41
|
+
return { txt: v.value };
|
|
42
|
+
}
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|
43
|
+
return { txt: format_val_text(v, tvs.term) };
|
|
44
|
+
}
|
|
45
|
+
return { txt: tvs.ranges.length + " intervals" };
|
|
46
|
+
}
|
|
47
|
+
function format_val_text(range, term) {
|
|
48
|
+
const x = '<span style="font-family:Times;font-style:italic;font-size:1em; vertical-align:top">x</span>';
|
|
49
|
+
if (range.startunbounded && range.stopunbounded) {
|
|
50
|
+
const inf = (sign = "") => `<span style='vertical-align: middle; font-size:1.1em; line-height: 0.9em'>${sign}\u221E</span>`;
|
|
51
|
+
const lt = `<span style='vertical-align: top; font-size: 0.9em'><</span>`;
|
|
52
|
+
return `<span>${inf("\uFE63")} ${lt} ${x} ${lt} ${inf("\uFE62")}</span>`;
|
|
53
|
+
}
|
|
54
|
+
const vc = term.valueConversion;
|
|
55
|
+
if (range.startunbounded)
|
|
56
|
+
return `${x} ${range.stopinclusive ? "≤" : "<"} ${vc ? convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.stop}`;
|
|
57
|
+
if (range.stopunbounded)
|
|
58
|
+
return `${x} ${range.startinclusive ? "≥" : ">"} ${vc ? convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.start}`;
|
|
59
|
+
let startName, stopName;
|
|
60
|
+
if (vc) {
|
|
61
|
+
startName = convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor);
|
|
62
|
+
stopName = convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor);
|
|
63
|
+
} else {
|
|
64
|
+
;
|
|
65
|
+
[startName, stopName] = niceNumLabels([range.start, range.stop]);
|
|
66
|
+
}
|
|
67
|
+
return `${startName}
|
|
68
|
+
${range.startinclusive ? "≤" : "<"}
|
|
69
|
+
${x}
|
|
70
|
+
${range.stopinclusive ? "≤" : "<"}
|
|
71
|
+
${stopName}`;
|
|
72
|
+
}
|
|
73
|
+
function getSelectRemovePos(j, tvs) {
|
|
74
|
+
return j - tvs.ranges.slice(0, j).filter((a) => a.start || a.stop).length;
|
|
75
|
+
}
|
|
76
|
+
async function fillMenu(self, div, tvs) {
|
|
77
|
+
const num_parent_div = div.append("div");
|
|
78
|
+
self.num_obj = {};
|
|
79
|
+
self.num_obj.num_div = num_parent_div.append("div").attr("class", "num_div").style("padding", "5px").style("color", "#000");
|
|
80
|
+
self.num_obj.plot_size = {
|
|
81
|
+
width: 450,
|
|
82
|
+
height: 100,
|
|
83
|
+
xpad: 10,
|
|
84
|
+
ypad: 20,
|
|
85
|
+
radius: 8
|
|
86
|
+
};
|
|
87
|
+
if (typeof self.opts.vocabApi.getViolinBox == "function") {
|
|
88
|
+
try {
|
|
89
|
+
const data = await self.opts.vocabApi.getViolinBox(
|
|
90
|
+
{
|
|
91
|
+
plotType: "violin",
|
|
92
|
+
tw: { term: tvs.term, q: { mode: "continuous" } },
|
|
93
|
+
// must supply this filter and override state filter in function, so the density plot will not be limited to range defined by current numeric tvs but will show whole range
|
|
94
|
+
filter: self.filter,
|
|
95
|
+
svgw: self.num_obj.plot_size.width,
|
|
96
|
+
radius: self.num_obj.plot_size.radius
|
|
97
|
+
},
|
|
98
|
+
self.opts.getCategoriesArguments
|
|
99
|
+
);
|
|
100
|
+
if (data.error) throw data.error;
|
|
101
|
+
if (data.max === null && data.min === null) {
|
|
102
|
+
throw `No data available under current filter conditions.`;
|
|
103
|
+
}
|
|
104
|
+
self.num_obj.density_data = data;
|
|
105
|
+
} catch (err) {
|
|
106
|
+
throw err;
|
|
107
|
+
}
|
|
108
|
+
} else {
|
|
109
|
+
self.num_obj.density_data = {};
|
|
110
|
+
}
|
|
111
|
+
if (self.num_obj.density_data.error) throw self.num_obj.density_data.error;
|
|
112
|
+
if (!self.num_obj.density_data.charts?.[""]?.plots?.[0]?.density?.bins) {
|
|
113
|
+
addRangeTableNoDensity(self, tvs);
|
|
114
|
+
return;
|
|
115
|
+
}
|
|
116
|
+
self.vr = new violinRenderer({
|
|
117
|
+
holder: self.num_obj.num_div,
|
|
118
|
+
rd: self.num_obj.density_data,
|
|
119
|
+
width: self.num_obj.plot_size.width,
|
|
120
|
+
radius: self.num_obj.plot_size.radius,
|
|
121
|
+
height: self.num_obj.plot_size.height,
|
|
122
|
+
// axis ticks are labeled in the term's user-facing unit, e.g. years and not days
|
|
123
|
+
scaleFactor: getValueConversionFactor(tvs.term)
|
|
124
|
+
});
|
|
125
|
+
self.vr.render();
|
|
126
|
+
self.num_obj.svg = self.vr.svg;
|
|
127
|
+
self.num_obj.range_table = self.num_obj.num_div.append("table").style("table-layout", "fixed").style("border-collapse", "collapse");
|
|
128
|
+
const ranges = [];
|
|
129
|
+
for (const [index, range] of tvs.ranges.entries()) {
|
|
130
|
+
range.index = index;
|
|
131
|
+
ranges.push(range);
|
|
132
|
+
}
|
|
133
|
+
self.num_obj.brush_g = self.vr.brushG.attr("class", "brush_g");
|
|
134
|
+
self.num_obj.xscale = self.vr.axisScale;
|
|
135
|
+
self.num_obj.ranges = ranges;
|
|
136
|
+
self.num_obj.brushes = [];
|
|
137
|
+
addBrushes(self);
|
|
138
|
+
addRangeTable(self);
|
|
139
|
+
if (!ranges.length) {
|
|
140
|
+
const callback = () => addRangeTable(self);
|
|
141
|
+
addNewBrush(self, "center", callback);
|
|
142
|
+
}
|
|
143
|
+
self.num_obj.brushes.forEach((brush) => brush.init());
|
|
144
|
+
await showCheckList_numeric(self, tvs, div);
|
|
145
|
+
}
|
|
146
|
+
function setTvsDefaults(tvs) {
|
|
147
|
+
if (!tvs.ranges) tvs.ranges = [];
|
|
148
|
+
}
|
|
149
|
+
function addRangeTableNoDensity(self, tvs) {
|
|
150
|
+
const termrange = tvs.term.range || {};
|
|
151
|
+
const range = tvs.ranges && tvs.ranges[0] ? tvs.ranges[0] : termrange;
|
|
152
|
+
range.min = "min" in tvs.term ? tvs.term.min : null;
|
|
153
|
+
range.max = "max" in tvs.term ? tvs.term.max : null;
|
|
154
|
+
const num_div = self.num_obj.num_div;
|
|
155
|
+
num_div.selectAll("*").remove();
|
|
156
|
+
const brush = {};
|
|
157
|
+
const holder = num_div.append("div").style("padding-left", "5px");
|
|
158
|
+
const rangeRow = holder.append("div").style("display", "flex").style("align-items", "center").style("column-gap", "5px");
|
|
159
|
+
const rangeLabel = rangeRow.append("span");
|
|
160
|
+
brush.equation_div = rangeRow.append("div");
|
|
161
|
+
brush.rangeInput = new NumericRangeInput(brush.equation_div, range, () => {
|
|
162
|
+
}, {
|
|
163
|
+
width: "125px",
|
|
164
|
+
scaleFactor: getValueConversionFactor(tvs.term)
|
|
165
|
+
});
|
|
166
|
+
const mafFilterMode = self.opts.isMafFilter ? tvs.term.mafFilterMode || "maf" : null;
|
|
167
|
+
if (mafFilterMode == "maf") {
|
|
168
|
+
rangeLabel.text("MAF Range (0-1)");
|
|
169
|
+
const depthRow = holder.append("div").style("display", "flex").style("align-items", "center").style("column-gap", "5px").style("margin-top", "5px");
|
|
170
|
+
depthRow.append("span").text("Minimum Total Depth");
|
|
171
|
+
brush.depthInput = depthRow.append("input").attr("type", "number").attr("min", 1).attr("step", 1).style("width", "125px").property("value", tvs.minAllelicDepth);
|
|
172
|
+
brush.apply_btn = addApplyButton(holder.append("div").style("margin-top", "10px"));
|
|
173
|
+
} else if (mafFilterMode == "totalDepth" || mafFilterMode == "altDepth") {
|
|
174
|
+
rangeLabel.text(mafFilterMode == "totalDepth" ? "Total Depth" : "Alt Allele Depth");
|
|
175
|
+
brush.apply_btn = addApplyButton(rangeRow);
|
|
176
|
+
} else {
|
|
177
|
+
rangeLabel.text("Range");
|
|
178
|
+
brush.apply_btn = addApplyButton(rangeRow);
|
|
179
|
+
}
|
|
180
|
+
function addApplyButton(holder2) {
|
|
181
|
+
return holder2.append("button").text("Apply").on("click", clickApply);
|
|
182
|
+
}
|
|
183
|
+
function clickApply() {
|
|
184
|
+
const r = brush.rangeInput.getRange();
|
|
185
|
+
if (!Number.isFinite(r.start) && !Number.isFinite(r.stop)) {
|
|
186
|
+
window.alert("Invalid range.");
|
|
187
|
+
return;
|
|
188
|
+
}
|
|
189
|
+
const new_tvs = { term: tvs.term, ranges: [r] };
|
|
190
|
+
if (brush.depthInput) {
|
|
191
|
+
const minAllelicDepth = Number(brush.depthInput.property("value"));
|
|
192
|
+
if (!Number.isFinite(minAllelicDepth)) {
|
|
193
|
+
window.alert("Minimum allelic depth must be a numeric value.");
|
|
194
|
+
return;
|
|
195
|
+
}
|
|
196
|
+
new_tvs.minAllelicDepth = Math.max(minAllelicDepth, 1);
|
|
197
|
+
}
|
|
198
|
+
self.dom.tip.hide();
|
|
199
|
+
self.opts.callback(new_tvs);
|
|
200
|
+
}
|
|
201
|
+
}
|
|
202
|
+
function addRangeTable(self) {
|
|
203
|
+
const brushes = self.num_obj.brushes;
|
|
204
|
+
const range_divs = self.num_obj.range_table.selectAll(".range_div").data(brushes);
|
|
205
|
+
range_divs.exit().each(function() {
|
|
206
|
+
select_default(this).style("opacity", 1).transition().duration(100).style("opacity", 0).remove();
|
|
207
|
+
});
|
|
208
|
+
range_divs.enter().append("tr").attr("class", "range_div").style("white-space", "nowrap").style("padding", "2px").transition().duration(200).each(function(brush, i) {
|
|
209
|
+
enterRange(self, this, brush, i);
|
|
210
|
+
});
|
|
211
|
+
}
|
|
212
|
+
function enterRange(self, tr, brush, i) {
|
|
213
|
+
if (!brush.range_tr) brush.range_tr = select_default(tr);
|
|
214
|
+
const range_tr = brush.range_tr;
|
|
215
|
+
const xscale = self.num_obj.xscale;
|
|
216
|
+
range_tr.append("td").style("margin-left", "10px").style("padding", "3px 10px").style("font-size", ".9em").text("Range " + (i + 1) + ": ");
|
|
217
|
+
brush.equation_td = range_tr.append("td").style("width", "150px");
|
|
218
|
+
brush.rangeInput = new NumericRangeInput(brush.equation_td, brush.range, apply, {
|
|
219
|
+
scaleFactor: getValueConversionFactor(self.tvs.term)
|
|
220
|
+
});
|
|
221
|
+
makeRangeButtons(self, brush);
|
|
222
|
+
if (i == 0) {
|
|
223
|
+
self.num_obj.range_table.append("tr").attr("class", "note_tr").append("td").attr("colspan", "3").append("div").style("font-size", ".8em").style("margin-left", "20px").style("font-style", "italic").style("color", "#888").html("Option 1: Drag the rectangle to select a range. Overlapping ranges will be merged.");
|
|
224
|
+
}
|
|
225
|
+
if (i == 0) {
|
|
226
|
+
self.num_obj.range_table.append("tr").attr("class", "note_tr").append("td").attr("colspan", "3").append("div").style("font-size", ".8em").style("margin-left", "20px").style("font-style", "italic").style("color", "#888").html(
|
|
227
|
+
`Option 2: Type in values to select a range.${self.tvs.term.valueConversion ? ` Values are in the unit of ${self.tvs.term.valueConversion.toUnit}.` : ""}`
|
|
228
|
+
);
|
|
229
|
+
}
|
|
230
|
+
async function apply(new_range) {
|
|
231
|
+
try {
|
|
232
|
+
brush.range = new_range;
|
|
233
|
+
const minvalue = self.num_obj.density_data.min;
|
|
234
|
+
const maxvalue = self.num_obj.density_data.max;
|
|
235
|
+
const start = new_range.value != void 0 ? new_range.value : new_range.start != void 0 ? new_range.start : minvalue;
|
|
236
|
+
const stop = new_range.value != void 0 ? new_range.value : new_range.stop != void 0 ? new_range.stop : maxvalue;
|
|
237
|
+
brush.elem.call(brush.d3brush).call(brush.d3brush.move, [start, stop].map(xscale));
|
|
238
|
+
} catch (e) {
|
|
239
|
+
window.alert(e);
|
|
240
|
+
}
|
|
241
|
+
}
|
|
242
|
+
function makeRangeButtons(self2, brush2) {
|
|
243
|
+
const buttons_td = brush2.range_tr.append("td");
|
|
244
|
+
const range = brush2.range;
|
|
245
|
+
brush2.apply_btn = buttons_td.append("button").style("margin-left", "10px").text("Apply").on("click", async () => {
|
|
246
|
+
self2.dom.tip.hide();
|
|
247
|
+
const new_range = brush2.rangeInput.parseRange();
|
|
248
|
+
const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
|
|
249
|
+
delete new_tvs.groupset_label;
|
|
250
|
+
if (self2.num_obj.ranges.length > 1) new_tvs.ranges = mergeOverlapRanges(self2, new_range);
|
|
251
|
+
else new_tvs.ranges[range.index] = new_range;
|
|
252
|
+
try {
|
|
253
|
+
validateNumericTvs(new_tvs);
|
|
254
|
+
self2.opts.callback(new_tvs);
|
|
255
|
+
} catch (ex) {
|
|
256
|
+
alert(ex);
|
|
257
|
+
}
|
|
258
|
+
});
|
|
259
|
+
buttons_td.append("button").attr("class", "sja_filter_tag_btn sjpp_delete_btn").style("display", self2.num_obj.ranges.length > 1 ? "inline-block" : "none").style("margin-left", "10px").style("text-transform", "uppercase").text("Delete").on("click", async () => {
|
|
260
|
+
const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
|
|
261
|
+
new_tvs.ranges.splice(range.index, 1);
|
|
262
|
+
self2.num_obj.ranges.pop();
|
|
263
|
+
self2.num_obj.brushes.pop();
|
|
264
|
+
self2.num_obj.num_div.select(".note_tr").remove();
|
|
265
|
+
addBrushes(self2);
|
|
266
|
+
addRangeTable(self2);
|
|
267
|
+
if (new_tvs.ranges.length) self2.opts.callback(new_tvs);
|
|
268
|
+
});
|
|
269
|
+
}
|
|
270
|
+
}
|
|
271
|
+
function mergeOverlapRanges(self, new_range) {
|
|
272
|
+
let ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
|
|
273
|
+
let merged_flag = false;
|
|
274
|
+
for (const [i, range] of ranges.entries()) {
|
|
275
|
+
if (!range.value && new_range.index != i) {
|
|
276
|
+
if (new_range.start <= range.start && new_range.stop >= range.stop) {
|
|
277
|
+
range.start = new_range.start;
|
|
278
|
+
range.stop = new_range.stop;
|
|
279
|
+
merged_flag = true;
|
|
280
|
+
} else if (new_range.start <= range.stop && new_range.stop >= range.stop) {
|
|
281
|
+
range.stop = new_range.stop;
|
|
282
|
+
merged_flag = true;
|
|
283
|
+
} else if (new_range.stop >= range.start && new_range.start <= range.start) {
|
|
284
|
+
range.start = new_range.start;
|
|
285
|
+
merged_flag = true;
|
|
286
|
+
} else if (new_range.start >= range.start && new_range.stop <= range.stop) {
|
|
287
|
+
merged_flag = true;
|
|
288
|
+
} else if (new_range.startunbounded) {
|
|
289
|
+
if (new_range.stop > range.stop) {
|
|
290
|
+
range.stop = new_range.stop;
|
|
291
|
+
}
|
|
292
|
+
delete range.start;
|
|
293
|
+
range.startunbounded = true;
|
|
294
|
+
merged_flag = true;
|
|
295
|
+
} else if (new_range.stopunbounded) {
|
|
296
|
+
if (new_range.start < range.start) {
|
|
297
|
+
range.start = new_range.start;
|
|
298
|
+
}
|
|
299
|
+
delete range.stop;
|
|
300
|
+
range.stopunbounded = true;
|
|
301
|
+
merged_flag = true;
|
|
302
|
+
}
|
|
303
|
+
}
|
|
304
|
+
}
|
|
305
|
+
if (merged_flag) {
|
|
306
|
+
if (new_range.index <= ranges.length - 1) ranges.splice(new_range.index, 1);
|
|
307
|
+
} else {
|
|
308
|
+
ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
|
|
309
|
+
if (new_range.index) ranges[new_range.index] = new_range;
|
|
310
|
+
else ranges.push(new_range);
|
|
311
|
+
}
|
|
312
|
+
return ranges;
|
|
313
|
+
}
|
|
314
|
+
async function showCheckList_numeric(self, tvs, div) {
|
|
315
|
+
if (!tvs.term.values) {
|
|
316
|
+
return;
|
|
317
|
+
}
|
|
318
|
+
const values = await self.opts.vocabApi.getNumericUncomputableCategories(tvs.term, self.filter);
|
|
319
|
+
const unannotated_cats = [];
|
|
320
|
+
const lst = values?.lst || values;
|
|
321
|
+
for (const cat of lst) {
|
|
322
|
+
const key = "key" in cat ? cat.key : cat.value;
|
|
323
|
+
if (!("key" in cat)) cat.key = key;
|
|
324
|
+
if (!("value" in cat)) cat.value = key;
|
|
325
|
+
if (key in tvs.term.values) {
|
|
326
|
+
cat.label = tvs.term.values[key].label;
|
|
327
|
+
unannotated_cats.push(cat);
|
|
328
|
+
}
|
|
329
|
+
}
|
|
330
|
+
const sortedVals = unannotated_cats.sort((a, b) => {
|
|
331
|
+
return b.samplecount - a.samplecount;
|
|
332
|
+
});
|
|
333
|
+
const unanno_div = div.append("div").style("padding", "5px").style("color", "#000");
|
|
334
|
+
const callback = (indexes) => {
|
|
335
|
+
try {
|
|
336
|
+
const new_tvs = JSON.parse(JSON.stringify(tvs));
|
|
337
|
+
delete new_tvs.groupset_label;
|
|
338
|
+
new_tvs.ranges = [
|
|
339
|
+
...new_tvs.ranges.filter((r) => !("value" in r)),
|
|
340
|
+
...indexes.map((i) => ({ value: sortedVals[i].value, label: sortedVals[i].label }))
|
|
341
|
+
];
|
|
342
|
+
self.dom.tip.hide();
|
|
343
|
+
if (new_tvs.ranges.length == 0) throw "select at least one range or category";
|
|
344
|
+
if (JSON.parse(JSON.stringify(tvs) != new_tvs)) {
|
|
345
|
+
try {
|
|
346
|
+
validateNumericTvs(new_tvs);
|
|
347
|
+
} catch (e) {
|
|
348
|
+
window.alert(e);
|
|
349
|
+
return;
|
|
350
|
+
}
|
|
351
|
+
self.opts.callback(new_tvs);
|
|
352
|
+
}
|
|
353
|
+
} catch (e) {
|
|
354
|
+
window.alert(e);
|
|
355
|
+
}
|
|
356
|
+
};
|
|
357
|
+
const values_table = self.makeValueTable(unanno_div, tvs, sortedVals, callback).node();
|
|
358
|
+
}
|
|
359
|
+
function validateNumericTvs(tvs) {
|
|
360
|
+
if (!tvs.term) throw "tvs.term is not defined";
|
|
361
|
+
if (!tvs.ranges) throw `.values[] missing for a term ${tvs.term.name}`;
|
|
362
|
+
if (!Array.isArray(tvs.ranges)) throw `.values[] is not an array for a term ${tvs.term.name}`;
|
|
363
|
+
if (!tvs.ranges.length) throw `no categories selected for ${tvs.term.name}`;
|
|
364
|
+
for (const range of tvs.ranges) {
|
|
365
|
+
if (range.value != void 0) {
|
|
366
|
+
if (!range.label) throw `.label missing for special category for a term ${tvs.term.name}`;
|
|
367
|
+
} else {
|
|
368
|
+
if (range.startunbounded) {
|
|
369
|
+
if (range.stopunbounded) throw `both start & stop are unbounded for a term ${tvs.term.name}`;
|
|
370
|
+
if (!Number.isFinite(range.stop)) throw `.stop undefined when start is unbounded for a term ${tvs.term.name}`;
|
|
371
|
+
} else if (range.stopunbounded) {
|
|
372
|
+
if (!Number.isFinite(range.start)) throw `.start undefined when stop is unbounded for a term ${tvs.term.name}`;
|
|
373
|
+
} else {
|
|
374
|
+
if (!Number.isFinite(range.start))
|
|
375
|
+
throw `.start undefined when start is not unbounded for a term ${tvs.term.name}`;
|
|
376
|
+
if (!Number.isFinite(range.stop)) throw `.stop undefined when stop is not unbounded for a term ${tvs.term.name}`;
|
|
377
|
+
if (range.start >= range.stop) throw `.start is not lower than stop for a term ${tvs.term.name}`;
|
|
378
|
+
}
|
|
379
|
+
}
|
|
380
|
+
}
|
|
381
|
+
}
|
|
382
|
+
|
|
383
|
+
export {
|
|
384
|
+
handler,
|
|
385
|
+
format_val_text
|
|
386
|
+
};
|
|
387
|
+
//# sourceMappingURL=chunk-SYPSS3JQ.js.map
|