@sjcrh/proteinpaint-client 2.221.0 → 2.222.0
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-QFXSYOYN.js +1362 -0
- package/dist/AggMatrixInput-7D4ZUYJK.js +402 -0
- package/dist/AggregateMatrix-NVSFZEW3.js +37 -0
- package/dist/AppHeader-5YJWBQP6.js +826 -0
- package/dist/BoxPlot-52WWBGKN.js +1229 -0
- package/dist/CorrelationVolcano-WS23O2JT.js +613 -0
- package/dist/Cuminc-5LJQYFEE.js +1217 -0
- package/dist/DE-Z5GBDXDU.js +85 -0
- package/dist/DEinput-3EAIVG5U.js +479 -0
- package/dist/DM-24NZPPS6.js +86 -0
- package/dist/DifferentialAnalysis-LRAPDIXB.js +236 -0
- package/dist/Disco-IDOTCKSD.js +3384 -0
- package/dist/Disco.UI-SLJKAA6N.js +239 -0
- package/dist/DmrPlot-5CRGQNM3.js +361 -0
- package/dist/GB-YCDIORF3.js +1388 -0
- package/dist/GSEA-IGWX3AG7.js +870 -0
- package/dist/GeneExpInput-PPOTCILZ.js +38 -0
- package/dist/Geomap-D5JPCJ5L.js +80 -0
- package/dist/HicApp-BNMMISAR.js +2240 -0
- package/dist/IDCViewer-IUPPLC5B.js +10808 -0
- package/dist/NumBinaryEditor-45I5YNHI.js +274 -0
- package/dist/NumBinaryEditor.unit.spec-5CJPIDH4.js +308 -0
- package/dist/NumContEditor-VMCE5LUM.js +100 -0
- package/dist/NumContEditor.unit.spec-DKNXTVXT.js +160 -0
- package/dist/NumCustomBinEditor-3EESV7PW.js +29 -0
- package/dist/NumCustomBinEditor.unit.spec-JPOK7BWZ.js +393 -0
- package/dist/NumDiscreteEditor-YZ3Q4J4M.js +165 -0
- package/dist/NumDiscreteEditor.unit.spec-V6NSX72E.js +229 -0
- package/dist/NumRegularBinEditor-6GI63X5V.js +29 -0
- package/dist/NumRegularBinEditor.unit.spec-KCGZLQ6T.js +274 -0
- package/dist/NumSplineEditor-OMJUFDSC.js +205 -0
- package/dist/NumSplineEditor.unit.spec-KUB2OITH.js +220 -0
- package/dist/NumericDensity-M4BIVIB3.js +29 -0
- package/dist/NumericDensity.unit.spec-G3GJMO4S.js +414 -0
- package/dist/NumericHandler-AMV4BETD.js +30 -0
- package/dist/NumericHandler.unit.spec-OJDMQQHX.js +225 -0
- package/dist/ProteomeInput-KB7YRARQ.js +610 -0
- package/dist/Regression-5KSKHUEJ.js +1412 -0
- package/dist/RunChart2-JJ4GQF44.js +744 -0
- package/dist/SC-LKCBWZQX.js +1290 -0
- package/dist/Violin-JRP7R53K.js +1092 -0
- package/dist/Volcano-BDD3PZ4T.js +2661 -0
- package/dist/Wsi-3C3ERYSG.js +636 -0
- package/dist/aboutSunburst-2T5SLCCB.js +93 -0
- package/dist/aboutSunburst-2T5SLCCB.js.map +7 -0
- package/dist/adSandbox-GFF6ZCRM.js +29 -0
- package/dist/animatedBubbleChart-PUPXCFJW.js +542 -0
- package/dist/app-EICBB32X.js +28 -0
- package/dist/app-Z7M3CFWA.js +38 -0
- package/dist/app.js +8 -8
- package/dist/bam-KQ5F34X5.js +872 -0
- package/dist/barchart-WRAEMD7B.js +38 -0
- package/dist/barchart2-5CX3CO4K.js +305 -0
- package/dist/block-53QIZEH3.js +6203 -0
- package/dist/block.init-4V3SIUNX.js +29 -0
- package/dist/block.mds.expressionrank-5YNTX35V.js +350 -0
- package/dist/block.mds.geneboxplot-X5OHLSWT.js +819 -0
- package/dist/block.mds.junction-QBJF6MFG.js +1534 -0
- package/dist/block.mds.svcnv-BNCMHJJB.js +6413 -0
- package/dist/block.svg-KQELYSEO.js +155 -0
- package/dist/block.tk.aicheck-5EDNNXGL.js +274 -0
- package/dist/block.tk.bam-FRPCGSAE.js +1906 -0
- package/dist/block.tk.bigwig.ui-XUJPSA6D.js +202 -0
- package/dist/block.tk.hicstraw-MVLZALFC.js +814 -0
- package/dist/block.tk.junction-DLZNHWSA.js +2353 -0
- package/dist/block.tk.junction.textmatrixui-J3EODITY.js +190 -0
- package/dist/block.tk.ld-4GEJ2Y2K.js +90 -0
- package/dist/block.tk.menu-NM7KA5GZ.js +1050 -0
- package/dist/block.tk.pgv-XFOJACVC.js +934 -0
- package/dist/brainImaging-WFRZQANN.js +550 -0
- package/dist/brainRegions-66KWCUF2.js +213 -0
- package/dist/bubbleHeatmap-VKLIJOMM.js +374 -0
- package/dist/cellTypeBubbleHeatmap-ZPCXC52I.js +274 -0
- package/dist/chunk-2NDFMFNM.js +134 -0
- package/dist/chunk-34AGCF72.js +203 -0
- package/dist/chunk-3KKI63GB.js +96 -0
- package/dist/chunk-3LUHZYIN.js +14 -0
- package/dist/chunk-4ASBDE27.js +26731 -0
- package/dist/chunk-4ASBDE27.js.map +7 -0
- package/dist/chunk-5XXYEKE2.js +237 -0
- package/dist/chunk-6C3USAU5.js +848 -0
- package/dist/chunk-7F2FBQRP.js +35 -0
- package/dist/chunk-7TRD7A2U.js +141 -0
- package/dist/chunk-AG2PISH4.js +257 -0
- package/dist/chunk-BGYZJXYZ.js +2799 -0
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- package/dist/chunk-QI4EZK7S.js +2941 -0
- package/dist/chunk-QNSB6O4W.js +70 -0
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- package/dist/chunk-R55JRVX7.js.map +7 -0
- package/dist/chunk-RSMASA5S.js +340 -0
- package/dist/chunk-S2BMWHFY.js +54 -0
- package/dist/chunk-SKL52OWF.js +466 -0
- package/dist/chunk-TRWUXFVB.js +102 -0
- package/dist/chunk-URCFNXAK.js +2008 -0
- package/dist/chunk-V2D7DA2M.js +194 -0
- package/dist/chunk-V2ZVMDBY.js +480 -0
- package/dist/chunk-VIFY62YA.js +243 -0
- package/dist/chunk-VZ2JWFSX.js +296 -0
- package/dist/chunk-W5GR42L2.js +159 -0
- package/dist/chunk-WDOX6A6T.js +1339 -0
- package/dist/chunk-XPL54FXR.js +6375 -0
- package/dist/chunk-XV3KWMG3.js +103 -0
- package/dist/chunk-YFFQ7JTJ.js +123 -0
- package/dist/chunk-ZD6AIFTS.js +1253 -0
- package/dist/chunk-ZDVYAOWC.js +516 -0
- package/dist/chunk-ZKIC65KR.js +2685 -0
- package/dist/chunk-ZPRI5XCE.js +82 -0
- package/dist/cohort-CI22KICX.js +66 -0
- package/dist/cohortSunburst-Z5DANXVS.js +402 -0
- package/dist/condition-GZOA7BZJ.js +323 -0
- package/dist/controls-OWC25VQN.js +30 -0
- package/dist/controls.config-UVC4Q7BS.js +30 -0
- package/dist/correlation-EBA5YVXA.js +91 -0
- package/dist/customdata.inputui-FZRZCPS3.js +280 -0
- package/dist/dataDownload-WIPQU33P.js +326 -0
- package/dist/databrowser.ui-6L6Q72W4.js +421 -0
- package/dist/dictionary-4VZEPGW5.js +109 -0
- package/dist/dnaMethylation-LN6THRNZ.js +29 -0
- package/dist/dnaMethylation.integration.spec-BXC6EPUV.js +194 -0
- package/dist/e2pca-EXFI4Q2Y.js +340 -0
- package/dist/ep-T7EZ34XV.js +1247 -0
- package/dist/expclust.gdc.spec-NAN4M75R.js +298 -0
- package/dist/facet-BJFUIWHK.js +556 -0
- package/dist/gb-CBC3PDKZ.js +77 -0
- package/dist/geneExpClustering-7JFY7TQT.js +240 -0
- package/dist/geneExpression-FOQOKD34.js +29 -0
- package/dist/geneExpression.unit.spec-XSFC5ZJP.js +151 -0
- package/dist/geneORA-KYPN66QU.js +269 -0
- package/dist/geneRanking-VEHFMRFL.js +544 -0
- package/dist/geneVariant-77V6FNJX.js +289 -0
- package/dist/geneVariant-BS3XZFYM.js +32 -0
- package/dist/geneVariant.integration.spec-US4OY3S5.js +672 -0
- package/dist/genefusion.ui-YNVTTLDE.js +299 -0
- package/dist/geneset-BH5MWNJQ.js +199 -0
- package/dist/genomeBrowser.spec-BFTGLRHG.js +272 -0
- package/dist/grin2-4AXUYJIL.js +66 -0
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- package/dist/hierCluster-IJHBVO2N.js +55 -0
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- package/dist/hierCluster.config-UUQEFTIG.js +32 -0
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- package/dist/hierCluster.interactivity-6CN5PNFR.js +45 -0
- package/dist/imagePlot-HKPPACFV.js +152 -0
- package/dist/importPlot-EMI6BVPR.js +8 -0
- package/dist/isoformExpression-SFBA3SY7.js +31 -0
- package/dist/isoformExpression.unit.spec-JKYWHGRN.js +233 -0
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- package/dist/launch.adhoc-R7SYX6GF.js +33 -0
- package/dist/leftlabel.sample-XJUDFAKS.js +253 -0
- package/dist/lollipop-V43BWGBT.js +162 -0
- package/dist/maf-KU44HXN3.js +451 -0
- package/dist/maftimeline-JPHVYTTU.js +583 -0
- package/dist/matrix-EABQEAMC.js +50 -0
- package/dist/matrix-HMLF5MDD.js +55 -0
- package/dist/matrix.config-RX5GWHTM.js +33 -0
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- package/dist/matrix.renderers-UGQXONTG.js +30 -0
- package/dist/matrix.sort.unit.spec-FJKIBDTU.js +464 -0
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- package/dist/matrix.unit.spec-7Y3BKFNQ.js +146 -0
- package/dist/mavb-ADD57P2Q.js +726 -0
- package/dist/mds.fimo-7WH5GVFZ.js +509 -0
- package/dist/mds.samplescatterplot-JYFOORUG.js +1545 -0
- package/dist/mds.survivalplot-2V4H3YZY.js +472 -0
- package/dist/multivalue-GLS3RPQ5.js +79 -0
- package/dist/oncomatrix-QA267TP2.js +286 -0
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- package/dist/plot.barplot-KBVYKICH.js +93 -0
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- package/dist/plot.brainImaging-GGUARYRT.js +51 -0
- package/dist/plot.disco-EP274JEW.js +98 -0
- package/dist/plot.ssgq-4VUH3ZWV.js +130 -0
- package/dist/plot.vaf2cov-2FPWA2FS.js +249 -0
- package/dist/polar2-7W5JRMB5.js +228 -0
- package/dist/profileForms-2IKL3SZU.js +937 -0
- package/dist/profilePlot-IURW2HQN.js +45 -0
- package/dist/proteinView-4ZRODQN3.js +1346 -0
- package/dist/proteomeCohortCompare-BK3FLW4Z.js +866 -0
- package/dist/pseudbulk.unit.spec-QGQCCHNF.js +82 -0
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- package/dist/selectGenomeWithTklst-LGBKEN3T.js +125 -0
- package/dist/singleCellCellType-ACQACM6W.js +29 -0
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- package/dist/singleCellGeneExpression-M4RPITJW.js +29 -0
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- /package/dist/{tvs.dt-FZSVMJOO.js.map → tvs.dt-XJ2MW2AP.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-PPFQIC42.js.map → tvs.dtcnv.categorical-H7FKTXH4.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-TV2IGHY4.js.map → tvs.dtcnv.continuous-JQ62ZHER.js.map} +0 -0
- /package/dist/{tvs.dtfusion-ON4BA4XJ.js.map → tvs.dtfusion-GC3DZ2BO.js.map} +0 -0
- /package/dist/{tvs.dtitd-VFNROOWQ.js.map → tvs.dtitd-3SHGIDIB.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-ZXOP37T5.js.map → tvs.dtsnvindel-BEDWZ4A2.js.map} +0 -0
- /package/dist/{tvs.dtsv-EUHPTW7J.js.map → tvs.dtsv-HRIMULVD.js.map} +0 -0
- /package/dist/{tvs.multivalue-NHVXZNDI.js.map → tvs.multivalue-5VC7BLSZ.js.map} +0 -0
- /package/dist/{tvs.numeric-FPWDPO3J.js.map → tvs.numeric-TGEC7G6A.js.map} +0 -0
- /package/dist/{tvs.samplelst-ZZHRNUP4.js.map → tvs.samplelst-Q6EYAUQZ.js.map} +0 -0
- /package/dist/{tvs.survival-F3KSG3U6.js.map → tvs.survival-NJ3DTZIG.js.map} +0 -0
- /package/dist/{tvs.termCollection-B37DZLDY.js.map → tvs.termCollection-TVVLPSTG.js.map} +0 -0
- /package/dist/{vocabulary-XNE5FFDK.js.map → vocabulary-A7ZBBU65.js.map} +0 -0
- /package/dist/{wsi.direct-3YH3QGQD.js.map → wsi.direct-JJGIAH6A.js.map} +0 -0
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import {
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2
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addGeneSearchbox,
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3
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getSCGEunit,
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4
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getSampleAssayInfo
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5
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} from "./chunk-4ASBDE27.js";
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6
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import {
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7
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Menu
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} from "./chunk-CNFTQSNE.js";
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9
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import {
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10
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SINGLECELL_GENE_EXPRESSION
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11
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} from "./chunk-WJLRU5OF.js";
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// termdb/handlers/singleCellGeneExpression.ts
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var SearchHandler = class {
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async init(opts) {
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this.validateOpts(opts);
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this.callback = opts.callback;
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this.app = opts.app;
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const sample = opts.usecase?.specialCase?.config?.sample;
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const { genes: geneList } = await getSampleAssayInfo(this.app.vocabApi, sample);
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const holder = opts.holder.append("div").style("padding", "10px 0px");
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const geneSearch = addGeneSearchbox({
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tip: new Menu({ padding: "0px" }),
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genome: opts.genomeObj,
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geneList,
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row: holder,
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searchOnly: "gene",
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callback: () => this.selectGene(geneSearch.geneSymbol, sample)
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});
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}
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/**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
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* with sample info not included.*/
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async selectGene(gene, sample) {
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if (!gene) throw new Error("No gene selected");
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const unit = getSCGEunit(this.app.vocabApi);
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const name = `${gene} ${unit}`;
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this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
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}
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validateOpts(opts) {
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if (opts.callback == null) throw new Error("callback is required");
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if (opts.app == null) throw new Error("app is required");
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if (opts.holder == null) throw new Error("holder is required");
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if (opts.genomeObj == null) throw new Error("genomeObj is required");
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if (opts.usecase == null) throw new Error("usecase is required");
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if (!opts.usecase?.specialCase?.config?.sample) {
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throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
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}
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}
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};
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export {
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SearchHandler
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};
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//# sourceMappingURL=chunk-C6PMNLN4.js.map
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import {
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addBrushes,
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addNewBrush
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} from "./chunk-OZUF7O2S.js";
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import {
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escapeHtml,
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niceNumLabels,
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violinRenderer
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} from "./chunk-4ASBDE27.js";
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import {
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convertUnits,
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getValueConversionFactor
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} from "./chunk-W5J3LTYS.js";
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import {
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NumericRangeInput
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} from "./chunk-PWYMHUXY.js";
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import {
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roundValueAuto
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} from "./chunk-TLT4YIG3.js";
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import {
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select_default
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} from "./chunk-I6Y4O3RR.js";
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// filter/tvs.numeric.js
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var handler = {
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type: "numeric",
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27
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term_name_gen,
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get_pill_label,
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getSelectRemovePos,
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fillMenu,
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setTvsDefaults
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};
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function term_name_gen(d) {
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const name = d.term.name;
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return name.length < 26 ? escapeHtml(name) : '<label title="' + escapeHtml(name) + '">' + escapeHtml(name.substring(0, 24)) + "...</label>";
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}
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function get_pill_label(tvs) {
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if (tvs.ranges.length == 1) {
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const v = tvs.ranges[0];
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if ("value" in v) {
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if (v.label) return { txt: escapeHtml(v.label) };
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if (tvs.term.values && tvs.term.values[v.value] && tvs.term.values[v.value].label)
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return { txt: escapeHtml(tvs.term.values[v.value].label) };
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console.error(`key "${v.value}" not found in values{} of ${tvs.term.name}`);
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return { txt: escapeHtml(v.value) };
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}
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return { txt: format_val_text(v, tvs.term) + mafDepthText(tvs) };
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}
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return { txt: tvs.ranges.length + " intervals" + mafDepthText(tvs) };
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}
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function mafDepthText(tvs) {
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if (tvs.term.mafFilterMode != "maf") return "";
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if (!Number.isFinite(tvs.minAllelicDepth) || tvs.minAllelicDepth < 1) return "";
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return `, Total depth ≥ ${tvs.minAllelicDepth}`;
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}
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56
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function format_val_text(range, term) {
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const x = '<span style="font-family:Times;font-style:italic;font-size:1em; vertical-align:top">x</span>';
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58
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if (range.startunbounded && range.stopunbounded) {
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59
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const inf = (sign = "") => `<span style='vertical-align: middle; font-size:1.1em; line-height: 0.9em'>${sign}\u221E</span>`;
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60
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const lt = `<span style='vertical-align: top; font-size: 0.9em'><</span>`;
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61
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return `<span>${inf("\uFE63")} ${lt} ${x} ${lt} ${inf("\uFE62")}</span>`;
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62
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}
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63
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const vc = term.valueConversion;
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if (range.startunbounded)
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65
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return `${x} ${range.stopinclusive ? "≤" : "<"} ${vc ? convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.stop}`;
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66
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if (range.stopunbounded)
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67
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return `${x} ${range.startinclusive ? "≥" : ">"} ${vc ? convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.start}`;
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68
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let startName, stopName;
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69
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if (vc) {
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70
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startName = convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor);
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71
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stopName = convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor);
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72
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} else {
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73
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;
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[startName, stopName] = niceNumLabels([range.start, range.stop]);
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75
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}
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76
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return `${startName}
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77
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${range.startinclusive ? "≤" : "<"}
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78
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${x}
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${range.stopinclusive ? "≤" : "<"}
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80
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${stopName}`;
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81
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}
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82
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function getSelectRemovePos(j, tvs) {
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83
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return j - tvs.ranges.slice(0, j).filter((a) => a.start || a.stop).length;
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84
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+
}
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85
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+
async function fillMenu(self, div, tvs) {
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86
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const num_parent_div = div.append("div");
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87
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self.num_obj = {};
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88
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self.num_obj.num_div = num_parent_div.append("div").attr("class", "num_div").style("padding", "5px").style("color", "#000");
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89
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self.num_obj.plot_size = {
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90
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width: 450,
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91
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height: 100,
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92
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xpad: 10,
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93
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ypad: 20,
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94
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radius: 8
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|
95
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};
|
|
96
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+
if (typeof self.opts.vocabApi.getViolinBox == "function") {
|
|
97
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+
try {
|
|
98
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+
const data = await self.opts.vocabApi.getViolinBox(
|
|
99
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{
|
|
100
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plotType: "violin",
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|
101
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+
tw: { term: tvs.term, q: { mode: "continuous" } },
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|
102
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+
// 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
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|
103
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filter: self.filter,
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104
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+
svgw: self.num_obj.plot_size.width,
|
|
105
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+
radius: self.num_obj.plot_size.radius
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106
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+
},
|
|
107
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+
self.opts.getCategoriesArguments
|
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108
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+
);
|
|
109
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+
if (data.error) throw data.error;
|
|
110
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+
if (data.max === null && data.min === null) {
|
|
111
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+
throw `No data available under current filter conditions.`;
|
|
112
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+
}
|
|
113
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+
self.num_obj.density_data = data;
|
|
114
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+
} catch (err) {
|
|
115
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+
throw err;
|
|
116
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+
}
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117
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+
} else {
|
|
118
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+
self.num_obj.density_data = {};
|
|
119
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+
}
|
|
120
|
+
if (self.num_obj.density_data.error) throw self.num_obj.density_data.error;
|
|
121
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+
if (!self.num_obj.density_data.charts?.[""]?.plots?.[0]?.density?.bins) {
|
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122
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+
addRangeTableNoDensity(self, tvs);
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|
123
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+
return;
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|
124
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+
}
|
|
125
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+
self.vr = new violinRenderer({
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|
126
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+
holder: self.num_obj.num_div,
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|
127
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+
rd: self.num_obj.density_data,
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|
128
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+
width: self.num_obj.plot_size.width,
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|
129
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+
radius: self.num_obj.plot_size.radius,
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|
130
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+
height: self.num_obj.plot_size.height,
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|
131
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+
// axis ticks are labeled in the term's user-facing unit, e.g. years and not days
|
|
132
|
+
scaleFactor: getValueConversionFactor(tvs.term)
|
|
133
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+
});
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134
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+
self.vr.render();
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|
135
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+
self.num_obj.svg = self.vr.svg;
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|
136
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+
self.num_obj.range_table = self.num_obj.num_div.append("table").style("table-layout", "fixed").style("border-collapse", "collapse");
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|
137
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+
const ranges = [];
|
|
138
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+
for (const [index, range] of tvs.ranges.entries()) {
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|
139
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range.index = index;
|
|
140
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+
ranges.push(range);
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|
141
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+
}
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|
142
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+
self.num_obj.brush_g = self.vr.brushG.attr("class", "brush_g");
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|
143
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+
self.num_obj.xscale = self.vr.axisScale;
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|
144
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+
self.num_obj.ranges = ranges;
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|
145
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+
self.num_obj.brushes = [];
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146
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+
addBrushes(self);
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147
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+
addRangeTable(self);
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148
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+
if (!ranges.length) {
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149
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+
const callback = () => addRangeTable(self);
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|
150
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+
addNewBrush(self, "center", callback);
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151
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+
}
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152
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+
self.num_obj.brushes.forEach((brush) => brush.init());
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153
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+
await showCheckList_numeric(self, tvs, div);
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154
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+
}
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|
155
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+
function setTvsDefaults(tvs) {
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|
156
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+
if (!tvs.ranges) tvs.ranges = [];
|
|
157
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+
}
|
|
158
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+
function addRangeTableNoDensity(self, tvs) {
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|
159
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+
const termrange = tvs.term.range || {};
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160
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+
const range = tvs.ranges && tvs.ranges[0] ? tvs.ranges[0] : termrange;
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161
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+
const num_div = self.num_obj.num_div;
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162
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+
num_div.selectAll("*").remove();
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163
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+
const brush = {};
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164
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+
const holder = num_div.append("div").style("padding-left", "5px");
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165
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+
const mafFilterMode = tvs.term.mafFilterMode;
|
|
166
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+
if (mafFilterMode == "maf" && tvs.term.child_ids?.length > 1) {
|
|
167
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+
const ids = tvs.term.child_ids;
|
|
168
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+
const list = ids.slice(0, -1).join(", ") + " and " + ids[ids.length - 1];
|
|
169
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+
holder.append("div").style("margin-bottom", "8px").style("font-size", ".9em").style("opacity", 0.7).text(`MAF is computed by summing allelic depths from ${list}`);
|
|
170
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+
}
|
|
171
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+
const rangeRow = holder.append("div").style("display", "flex").style("align-items", "center").style("column-gap", "5px");
|
|
172
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+
const rangeLabel = rangeRow.append("span");
|
|
173
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+
brush.equation_div = rangeRow.append("div");
|
|
174
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+
brush.rangeInput = new NumericRangeInput(brush.equation_div, range, () => {
|
|
175
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+
}, {
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|
176
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+
width: "125px",
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|
177
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+
scaleFactor: getValueConversionFactor(tvs.term),
|
|
178
|
+
// without a density plot, the term's declared bounds are the only check of a typed range
|
|
179
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+
min: tvs.term.min,
|
|
180
|
+
max: tvs.term.max
|
|
181
|
+
});
|
|
182
|
+
if (mafFilterMode == "maf") {
|
|
183
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+
rangeLabel.text("MAF Range (0-1)");
|
|
184
|
+
const depthRow = holder.append("div").style("display", "flex").style("align-items", "center").style("column-gap", "5px").style("margin-top", "5px");
|
|
185
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+
depthRow.append("span").text("Minimum Total Depth");
|
|
186
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+
brush.depthInput = depthRow.append("input").attr("type", "number").attr("min", 1).attr("step", 1).style("width", "125px").property("value", Number.isFinite(tvs.minAllelicDepth) ? tvs.minAllelicDepth : "");
|
|
187
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+
brush.apply_btn = addApplyButton(holder.append("div").style("margin-top", "10px"));
|
|
188
|
+
} else if (mafFilterMode == "value") {
|
|
189
|
+
rangeLabel.text("Range");
|
|
190
|
+
brush.apply_btn = addApplyButton(rangeRow);
|
|
191
|
+
} else if (mafFilterMode == "totalDepth" || mafFilterMode == "altDepth") {
|
|
192
|
+
rangeLabel.text(mafFilterMode == "totalDepth" ? "Total Depth" : "Alt Allele Depth");
|
|
193
|
+
brush.apply_btn = addApplyButton(rangeRow);
|
|
194
|
+
} else {
|
|
195
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+
rangeLabel.text("Range");
|
|
196
|
+
brush.apply_btn = addApplyButton(rangeRow);
|
|
197
|
+
}
|
|
198
|
+
if (mafFilterMode) brush.rangeInput.getInput().node().focus();
|
|
199
|
+
function addApplyButton(holder2) {
|
|
200
|
+
return holder2.append("button").text("Apply").on("click", clickApply);
|
|
201
|
+
}
|
|
202
|
+
function clickApply() {
|
|
203
|
+
const r = brush.rangeInput.getRange();
|
|
204
|
+
if (!Number.isFinite(r.start) && !Number.isFinite(r.stop)) {
|
|
205
|
+
window.alert("Invalid range.");
|
|
206
|
+
return;
|
|
207
|
+
}
|
|
208
|
+
const new_tvs = { term: tvs.term, ranges: [r] };
|
|
209
|
+
if (brush.depthInput) {
|
|
210
|
+
const str = brush.depthInput.property("value").trim();
|
|
211
|
+
if (str) {
|
|
212
|
+
const minAllelicDepth = Number(str);
|
|
213
|
+
if (!Number.isFinite(minAllelicDepth)) {
|
|
214
|
+
window.alert("Minimum allelic depth must be a numeric value.");
|
|
215
|
+
return;
|
|
216
|
+
}
|
|
217
|
+
new_tvs.minAllelicDepth = Math.max(minAllelicDepth, 1);
|
|
218
|
+
}
|
|
219
|
+
}
|
|
220
|
+
self.dom.tip.hide();
|
|
221
|
+
self.opts.callback(new_tvs);
|
|
222
|
+
}
|
|
223
|
+
}
|
|
224
|
+
function addRangeTable(self) {
|
|
225
|
+
const brushes = self.num_obj.brushes;
|
|
226
|
+
const range_divs = self.num_obj.range_table.selectAll(".range_div").data(brushes);
|
|
227
|
+
range_divs.exit().each(function() {
|
|
228
|
+
select_default(this).style("opacity", 1).transition().duration(100).style("opacity", 0).remove();
|
|
229
|
+
});
|
|
230
|
+
range_divs.enter().append("tr").attr("class", "range_div").style("white-space", "nowrap").style("padding", "2px").transition().duration(200).each(function(brush, i) {
|
|
231
|
+
enterRange(self, this, brush, i);
|
|
232
|
+
});
|
|
233
|
+
}
|
|
234
|
+
function enterRange(self, tr, brush, i) {
|
|
235
|
+
if (!brush.range_tr) brush.range_tr = select_default(tr);
|
|
236
|
+
const range_tr = brush.range_tr;
|
|
237
|
+
const xscale = self.num_obj.xscale;
|
|
238
|
+
range_tr.append("td").style("margin-left", "10px").style("padding", "3px 10px").style("font-size", ".9em").text("Range " + (i + 1) + ": ");
|
|
239
|
+
brush.equation_td = range_tr.append("td").style("width", "150px");
|
|
240
|
+
brush.rangeInput = new NumericRangeInput(brush.equation_td, brush.range, apply, {
|
|
241
|
+
scaleFactor: getValueConversionFactor(self.tvs.term)
|
|
242
|
+
});
|
|
243
|
+
makeRangeButtons(self, brush);
|
|
244
|
+
if (i == 0) {
|
|
245
|
+
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.");
|
|
246
|
+
}
|
|
247
|
+
if (i == 0) {
|
|
248
|
+
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(
|
|
249
|
+
`Option 2: Type in values to select a range.${self.tvs.term.valueConversion ? ` Values are in the unit of ${self.tvs.term.valueConversion.toUnit}.` : ""}`
|
|
250
|
+
);
|
|
251
|
+
}
|
|
252
|
+
function apply(new_range) {
|
|
253
|
+
const minvalue = self.num_obj.density_data.min;
|
|
254
|
+
const maxvalue = self.num_obj.density_data.max;
|
|
255
|
+
validateRangeInData(self, new_range);
|
|
256
|
+
brush.range = new_range;
|
|
257
|
+
const start = new_range.value != void 0 ? new_range.value : new_range.start != void 0 ? new_range.start : minvalue;
|
|
258
|
+
const stop = new_range.value != void 0 ? new_range.value : new_range.stop != void 0 ? new_range.stop : maxvalue;
|
|
259
|
+
const clamp = (v) => Math.min(Math.max(v, minvalue), maxvalue);
|
|
260
|
+
brush.elem.call(brush.d3brush).call(brush.d3brush.move, [clamp(start), clamp(stop)].map(xscale));
|
|
261
|
+
}
|
|
262
|
+
function makeRangeButtons(self2, brush2) {
|
|
263
|
+
const buttons_td = brush2.range_tr.append("td");
|
|
264
|
+
const range = brush2.range;
|
|
265
|
+
brush2.apply_btn = buttons_td.append("button").style("margin-left", "10px").text("Apply").attr("data-testid", "sjpp-tvsnumeric-range-apply").on("click", async () => {
|
|
266
|
+
try {
|
|
267
|
+
const new_range = brush2.rangeInput.parseRange();
|
|
268
|
+
const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
|
|
269
|
+
delete new_tvs.groupset_label;
|
|
270
|
+
if (self2.num_obj.ranges.length > 1) new_tvs.ranges = mergeOverlapRanges(self2, new_range);
|
|
271
|
+
else new_tvs.ranges[range.index] = new_range;
|
|
272
|
+
validateNumericTvs(new_tvs);
|
|
273
|
+
self2.dom.tip.hide();
|
|
274
|
+
self2.opts.callback(new_tvs);
|
|
275
|
+
} catch (ex) {
|
|
276
|
+
alert(ex);
|
|
277
|
+
}
|
|
278
|
+
});
|
|
279
|
+
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 () => {
|
|
280
|
+
const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
|
|
281
|
+
new_tvs.ranges.splice(range.index, 1);
|
|
282
|
+
self2.num_obj.ranges.pop();
|
|
283
|
+
self2.num_obj.brushes.pop();
|
|
284
|
+
self2.num_obj.num_div.select(".note_tr").remove();
|
|
285
|
+
addBrushes(self2);
|
|
286
|
+
addRangeTable(self2);
|
|
287
|
+
if (new_tvs.ranges.length) self2.opts.callback(new_tvs);
|
|
288
|
+
});
|
|
289
|
+
}
|
|
290
|
+
}
|
|
291
|
+
function mergeOverlapRanges(self, new_range) {
|
|
292
|
+
let ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
|
|
293
|
+
let merged_flag = false;
|
|
294
|
+
for (const [i, range] of ranges.entries()) {
|
|
295
|
+
if (!range.value && new_range.index != i) {
|
|
296
|
+
if (new_range.start <= range.start && new_range.stop >= range.stop) {
|
|
297
|
+
range.start = new_range.start;
|
|
298
|
+
range.stop = new_range.stop;
|
|
299
|
+
merged_flag = true;
|
|
300
|
+
} else if (new_range.start <= range.stop && new_range.stop >= range.stop) {
|
|
301
|
+
range.stop = new_range.stop;
|
|
302
|
+
merged_flag = true;
|
|
303
|
+
} else if (new_range.stop >= range.start && new_range.start <= range.start) {
|
|
304
|
+
range.start = new_range.start;
|
|
305
|
+
merged_flag = true;
|
|
306
|
+
} else if (new_range.start >= range.start && new_range.stop <= range.stop) {
|
|
307
|
+
merged_flag = true;
|
|
308
|
+
} else if (new_range.startunbounded) {
|
|
309
|
+
if (new_range.stop > range.stop) {
|
|
310
|
+
range.stop = new_range.stop;
|
|
311
|
+
}
|
|
312
|
+
delete range.start;
|
|
313
|
+
range.startunbounded = true;
|
|
314
|
+
merged_flag = true;
|
|
315
|
+
} else if (new_range.stopunbounded) {
|
|
316
|
+
if (new_range.start < range.start) {
|
|
317
|
+
range.start = new_range.start;
|
|
318
|
+
}
|
|
319
|
+
delete range.stop;
|
|
320
|
+
range.stopunbounded = true;
|
|
321
|
+
merged_flag = true;
|
|
322
|
+
}
|
|
323
|
+
}
|
|
324
|
+
}
|
|
325
|
+
if (merged_flag) {
|
|
326
|
+
if (new_range.index <= ranges.length - 1) ranges.splice(new_range.index, 1);
|
|
327
|
+
} else {
|
|
328
|
+
ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
|
|
329
|
+
if (new_range.index) ranges[new_range.index] = new_range;
|
|
330
|
+
else ranges.push(new_range);
|
|
331
|
+
}
|
|
332
|
+
return ranges;
|
|
333
|
+
}
|
|
334
|
+
async function showCheckList_numeric(self, tvs, div) {
|
|
335
|
+
if (!tvs.term.values) {
|
|
336
|
+
return;
|
|
337
|
+
}
|
|
338
|
+
const values = await self.opts.vocabApi.getNumericUncomputableCategories(tvs.term, self.filter);
|
|
339
|
+
const unannotated_cats = [];
|
|
340
|
+
const lst = values?.lst || values;
|
|
341
|
+
for (const cat of lst) {
|
|
342
|
+
const key = "key" in cat ? cat.key : cat.value;
|
|
343
|
+
if (!("key" in cat)) cat.key = key;
|
|
344
|
+
if (!("value" in cat)) cat.value = key;
|
|
345
|
+
if (key in tvs.term.values) {
|
|
346
|
+
cat.label = tvs.term.values[key].label;
|
|
347
|
+
unannotated_cats.push(cat);
|
|
348
|
+
}
|
|
349
|
+
}
|
|
350
|
+
const sortedVals = unannotated_cats.sort((a, b) => {
|
|
351
|
+
return b.samplecount - a.samplecount;
|
|
352
|
+
});
|
|
353
|
+
const unanno_div = div.append("div").style("padding", "5px").style("color", "#000");
|
|
354
|
+
const callback = (indexes) => {
|
|
355
|
+
try {
|
|
356
|
+
const new_tvs = JSON.parse(JSON.stringify(tvs));
|
|
357
|
+
delete new_tvs.groupset_label;
|
|
358
|
+
new_tvs.ranges = [
|
|
359
|
+
...new_tvs.ranges.filter((r) => !("value" in r)),
|
|
360
|
+
...indexes.map((i) => ({ value: sortedVals[i].value, label: sortedVals[i].label }))
|
|
361
|
+
];
|
|
362
|
+
self.dom.tip.hide();
|
|
363
|
+
if (new_tvs.ranges.length == 0) throw "select at least one range or category";
|
|
364
|
+
if (JSON.parse(JSON.stringify(tvs) != new_tvs)) {
|
|
365
|
+
try {
|
|
366
|
+
validateNumericTvs(new_tvs);
|
|
367
|
+
} catch (e) {
|
|
368
|
+
window.alert(e);
|
|
369
|
+
return;
|
|
370
|
+
}
|
|
371
|
+
self.opts.callback(new_tvs);
|
|
372
|
+
}
|
|
373
|
+
} catch (e) {
|
|
374
|
+
window.alert(e);
|
|
375
|
+
}
|
|
376
|
+
};
|
|
377
|
+
const values_table = self.makeValueTable(unanno_div, tvs, sortedVals, callback).node();
|
|
378
|
+
}
|
|
379
|
+
function validateRangeInData(self, range) {
|
|
380
|
+
if (range.value != void 0) return;
|
|
381
|
+
const { min, max } = self.num_obj.density_data;
|
|
382
|
+
if (!Number.isFinite(min) || !Number.isFinite(max)) return;
|
|
383
|
+
const aboveMax = !range.startunbounded && (range.start > max || range.start == max && !range.startinclusive);
|
|
384
|
+
const belowMin = !range.stopunbounded && (range.stop < min || range.stop == min && !range.stopinclusive);
|
|
385
|
+
if (!aboveMax && !belowMin) return;
|
|
386
|
+
const sf = getValueConversionFactor(self.tvs.term);
|
|
387
|
+
const [minLabel, maxLabel] = [min, max].map((v) => roundValueAuto(v * sf));
|
|
388
|
+
throw `The range is outside of the data, which ranges from ${minLabel} to ${maxLabel}`;
|
|
389
|
+
}
|
|
390
|
+
function validateNumericTvs(tvs) {
|
|
391
|
+
if (!tvs.term) throw "tvs.term is not defined";
|
|
392
|
+
if (!tvs.ranges) throw `.values[] missing for a term ${tvs.term.name}`;
|
|
393
|
+
if (!Array.isArray(tvs.ranges)) throw `.values[] is not an array for a term ${tvs.term.name}`;
|
|
394
|
+
if (!tvs.ranges.length) throw `no categories selected for ${tvs.term.name}`;
|
|
395
|
+
for (const range of tvs.ranges) {
|
|
396
|
+
if (range.value != void 0) {
|
|
397
|
+
if (!range.label) throw `.label missing for special category for a term ${tvs.term.name}`;
|
|
398
|
+
} else {
|
|
399
|
+
if (range.startunbounded) {
|
|
400
|
+
if (range.stopunbounded) throw `both start & stop are unbounded for a term ${tvs.term.name}`;
|
|
401
|
+
if (!Number.isFinite(range.stop)) throw `.stop undefined when start is unbounded for a term ${tvs.term.name}`;
|
|
402
|
+
} else if (range.stopunbounded) {
|
|
403
|
+
if (!Number.isFinite(range.start)) throw `.start undefined when stop is unbounded for a term ${tvs.term.name}`;
|
|
404
|
+
} else {
|
|
405
|
+
if (!Number.isFinite(range.start))
|
|
406
|
+
throw `.start undefined when start is not unbounded for a term ${tvs.term.name}`;
|
|
407
|
+
if (!Number.isFinite(range.stop)) throw `.stop undefined when stop is not unbounded for a term ${tvs.term.name}`;
|
|
408
|
+
if (range.start >= range.stop) throw `.start is not lower than stop for a term ${tvs.term.name}`;
|
|
409
|
+
}
|
|
410
|
+
}
|
|
411
|
+
}
|
|
412
|
+
}
|
|
413
|
+
|
|
414
|
+
export {
|
|
415
|
+
handler,
|
|
416
|
+
format_val_text
|
|
417
|
+
};
|
|
418
|
+
//# sourceMappingURL=chunk-CSYXTB7F.js.map
|
|
@@ -0,0 +1,55 @@
|
|
|
1
|
+
import {
|
|
2
|
+
colorinframe
|
|
3
|
+
} from "./chunk-4ASBDE27.js";
|
|
4
|
+
import {
|
|
5
|
+
IN_frame,
|
|
6
|
+
OUT_frame
|
|
7
|
+
} from "./chunk-WJLRU5OF.js";
|
|
8
|
+
|
|
9
|
+
// src/spliceevent.phrase.js
|
|
10
|
+
function spliceevent_phrase_default(evt) {
|
|
11
|
+
const htmls = [];
|
|
12
|
+
if (evt.isaltexon || evt.isskipexon) {
|
|
13
|
+
const exonstart = Math.min(...evt.skippedexon);
|
|
14
|
+
const exonstop = Math.max(...evt.skippedexon);
|
|
15
|
+
htmls.push(
|
|
16
|
+
'<div style="display:inline-block">' + (exonstart == exonstop ? "exon " + (exonstart + 1) : "exons " + (exonstart + 1) + "-" + (exonstop + 1)) + " " + (evt.isaltexon ? "alternative usage" : "skipping") + "</div>"
|
|
17
|
+
);
|
|
18
|
+
if (evt.isaltexon) {
|
|
19
|
+
htmls.push(
|
|
20
|
+
"<div class=sja_tinylogo_body>" + evt.gmB.isoform + ", " + evt.gmA.isoform + "</div><div class=sja_tinylogo_head>ISOFORMS</div>"
|
|
21
|
+
);
|
|
22
|
+
} else {
|
|
23
|
+
htmls.push("<div class=sja_tinylogo_body>" + evt.gm.isoform + "</div><div class=sja_tinylogo_head>ISOFORM</div>");
|
|
24
|
+
}
|
|
25
|
+
if (evt.junctionB.data) {
|
|
26
|
+
htmls.push(
|
|
27
|
+
"<div class=sja_tinylogo_body>" + evt.junctionB.data.length + "</div><div class=sja_tinylogo_head>SAMPLE" + (evt.junctionB.data.length > 1 ? "S" : "") + "</div>"
|
|
28
|
+
);
|
|
29
|
+
}
|
|
30
|
+
htmls.push("<div class=sja_tinylogo_body>" + evt.percentage + " %</div><div class=sja_tinylogo_head>PERCENT</div>");
|
|
31
|
+
if (evt.framenocheck) {
|
|
32
|
+
if (evt.utr3) {
|
|
33
|
+
htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">3' UTR</div>`);
|
|
34
|
+
} else if (evt.utr5) {
|
|
35
|
+
htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">5' UTR</div>`);
|
|
36
|
+
}
|
|
37
|
+
} else if (evt.frame == IN_frame) {
|
|
38
|
+
htmls.push(
|
|
39
|
+
'<div class=sja_tinylogo_body style="background-color:' + colorinframe + ';color:white">IN</div><div class=sja_tinylogo_head>FRAME</div>'
|
|
40
|
+
);
|
|
41
|
+
} else if (evt.frame == OUT_frame) {
|
|
42
|
+
htmls.push("<div class=sja_tinylogo_body>OUT</div><div class=sja_tinylogo_head>FRAME</div>");
|
|
43
|
+
} else {
|
|
44
|
+
htmls.push("<div class=sja_tinylogo_body>?</div><div class=sja_tinylogo_head>FRAME</div>");
|
|
45
|
+
}
|
|
46
|
+
} else {
|
|
47
|
+
return "unknown event type!!";
|
|
48
|
+
}
|
|
49
|
+
return htmls.join(" ");
|
|
50
|
+
}
|
|
51
|
+
|
|
52
|
+
export {
|
|
53
|
+
spliceevent_phrase_default
|
|
54
|
+
};
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|
55
|
+
//# sourceMappingURL=chunk-DFKTWNCC.js.map
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