@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/chunk-YDIIKD7O.js

@@ -1,102 +0,0 @@
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist,
-  getDNAMethUnit,
-  sayerror
-} from "./chunk-PEKCVKJK.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  DNA_METHYLATION
-} from "./chunk-WJLRU5OF.js";
-
-// termdb/handlers/dnaMethylation.ts
-var SearchHandler = class {
-  init(opts) {
-    this.opts = opts;
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("margin", "10px 0px");
-    this.dom = {};
-    this.dom.errDiv = holder.append("div").style("margin", "5px 0px").style("display", "none");
-    this.dom.geneSearchDiv = holder.append("div");
-    this.dom.blockDiv = holder.append("div").style("display", "none").style("margin", "15px 4px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: this.dom.geneSearchDiv,
-      callback: async () => {
-        try {
-          this.dom.errDiv.style("display", "none");
-          await this.handleGeneSearch(geneSearch);
-        } catch (e) {
-          this.dom.errDiv.style("display", "block");
-          sayerror(this.dom.errDiv, "Error: " + (e.message || e));
-          if (e.stack) console.log(e.stack);
-        }
-      }
-    });
-  }
-  async handleGeneSearch(geneSearch) {
-    if (geneSearch.geneSymbol) {
-      const { chr, start, stop } = geneSearch;
-      if (!chr || !Number.isInteger(start) || !Number.isInteger(stop))
-        throw new Error("unable to retrieve gene coordinate");
-      this.dom.blockDiv.selectAll("*").remove();
-      this.dom.blockDiv.style("display", "block");
-      this.dom.blockDiv.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
-      const arg = {
-        holder: this.dom.blockDiv,
-        genome: this.opts.genomeObj,
-        // genome obj
-        chr,
-        start,
-        stop,
-        tklst: [],
-        nobox: true,
-        width: 500,
-        hidegenelegend: true,
-        debugmode: this.opts.debug
-      };
-      first_genetrack_tolist(this.opts.genomeObj, arg.tklst);
-      const _ = await import("./block-VMVJH77F.js");
-      this.blockInstance = new _.Block(arg);
-      this.dom.submitBtn = this.dom.blockDiv.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
-        const { chr: chr2, start: start2, stop: stop2 } = this.blockInstance.rglst[0];
-        const term = this.makeTerm({ chr: chr2, start: start2, stop: stop2 });
-        await this.callback(term);
-      });
-    } else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
-      const { chr } = geneSearch;
-      let { start, stop } = geneSearch;
-      if (geneSearch.actualposition?.len <= 1) {
-        start = geneSearch.actualposition.position;
-        stop = start + 1;
-      }
-      const term = this.makeTerm({ chr, start, stop });
-      await this.callback(term);
-    } else {
-      throw new Error("invalid gene search input");
-    }
-  }
-  makeTerm(opts) {
-    const { chr, start, stop } = opts;
-    if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
-    const unit = getDNAMethUnit("region", this.app.vocabApi);
-    const term = {
-      chr,
-      start,
-      stop,
-      type: DNA_METHYLATION,
-      unit,
-      genomicFeatureType: "region"
-    };
-    return term;
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-YDIIKD7O.js.map

package/dist/chunk-YLGSRK75.js

@@ -1,102 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-Z53VY5JV.js";
-import {
-  fillTermWrapper
-} from "./chunk-PEKCVKJK.js";
-import {
-  dictionaryNumericTypes,
-  numericTypes
-} from "./chunk-JHLF2ZC2.js";
-import {
-  copyMerge
-} from "./chunk-HBNB5TRH.js";
-
-// plots/matrix/hierCluster.config.js
-async function getPlotConfig2(opts = {}, app) {
-  opts.chartType = "hierCluster";
-  if (dictionaryNumericTypes.has(opts.dataType) || opts.dataType == "numericDictTerm") {
-    const grp = opts.termgroups?.find((g) => g.type == "hierCluster");
-    for (const tw of grp?.lst || []) tw.q = { ...tw.q, mode: "continuous" };
-  }
-  const config = await getPlotConfig(opts, app);
-  delete config.genes;
-  if (config.dataType == "numericDictTerm") {
-    const lst = config.termgroups?.find((g) => g.type == "hierCluster")?.lst;
-    config.dataType = lst?.[0]?.term?.type || "float";
-  }
-  config.settings.hierCluster = {
-    /* type of data used for clustering
-    exciting todo: (to introduce new dt values)
-    - gene dependency
-    - numeric dic term
-    - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
-    - metabolite
-    */
-    dataType: config.dataType,
-    // adjust the default group name based on automatically detected term types
-    // Done in matrix.cells.js: setHierClusterCellProps
-    // termGroupName: 'Expression',
-    clusterSamples: true,
-    clusterRows: true,
-    clusterMethod: "average",
-    // complete
-    distanceMethod: "euclidean",
-    zScoreCap: 5,
-    zScoreTransformation: true,
-    xDendrogramHeight: 100,
-    yDendrogramHeight: 200,
-    colorScale: "blueWhiteRed"
-  };
-  const overrides = app.vocabApi.termdbConfig.hierCluster || {};
-  const numericDictTermClusterOverrides = dictionaryNumericTypes.has(config.dataType) && app.vocabApi.termdbConfig.numericDictTermCluster ? app.vocabApi.termdbConfig.numericDictTermCluster : {};
-  copyMerge(
-    config.settings.hierCluster,
-    overrides.settings,
-    opts.settings?.hierCluster || {},
-    numericDictTermClusterOverrides.settings
-  );
-  {
-    const c = config.settings.hierCluster.colorScale;
-    if (!c) throw "colorScale missing";
-  }
-  config.settings.matrix.collabelpos = "top";
-  const termGroupName = config.settings.hierCluster.termGroupName;
-  const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
-    name: termGroupName
-  };
-  hcTermGroup.type = "hierCluster";
-  if (!hcTermGroup.lst?.length) {
-    if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
-    const promises = [];
-    for (const i of opts.terms) {
-      const tw = i.term ? i : { term: i };
-      if (!tw.term.type) {
-        if (config.dataType && numericTypes.has(config.dataType)) {
-          tw.term.type = config.dataType;
-        } else {
-          throw `term type missing and cannot be assigned by dataType '${config.dataType}'`;
-        }
-      } else if (!numericTypes.has(tw.term.type)) {
-        throw "term type is not numeric";
-      } else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
-        throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
-      }
-      if (dictionaryNumericTypes.has(tw.term.type)) tw.q = { ...tw.q, mode: "continuous" };
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    hcTermGroup.lst = await Promise.all(promises);
-    if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
-  }
-  config.settings.matrix.maxSample = 1e5;
-  return config;
-}
-function canTermBeInHierGrp(grpType, twType) {
-  if (dictionaryNumericTypes.has(grpType) && dictionaryNumericTypes.has(twType)) return true;
-  return twType == grpType;
-}
-
-export {
-  getPlotConfig2 as getPlotConfig
-};
-//# sourceMappingURL=chunk-YLGSRK75.js.map

package/dist/chunk-YR6EXI2K.js

@@ -1,184 +0,0 @@
-import {
-  __glob
-} from "./chunk-HS5PO5ZQ.js";
-
-// import("../plots/**/*.js") in plots/importPlot.js
-var globImport_plots_js = __glob({
-  "../plots/controls.btns.js": () => import("./controls.btns-6AKLIWOG.js"),
-  "../plots/controls.config.js": () => import("./controls.config-ZKMQI27Q.js"),
-  "../plots/controls.js": () => import("./controls-MMMRBTZL.js"),
-  "../plots/dictionary.js": () => import("./dictionary-TQUVCHIN.js"),
-  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-OVXFKEIU.js"),
-  "../plots/geneExpression.js": () => import("./geneExpression-KPUOZ4PT.js"),
-  "../plots/geneORA.js": () => import("./geneORA-GNXKCN45.js"),
-  "../plots/geneset.js": () => import("./geneset-MBMCJNXT.js"),
-  "../plots/hierCluster.js": () => import("./hierCluster-L3LYQZQL.js"),
-  "../plots/importPlot.js": () => import("./importPlot-3SSCNROC.js"),
-  "../plots/matrix.js": () => import("./matrix-A6BNFCIH.js"),
-  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-VZBV5QIO.js"),
-  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-EA7WVIQR.js"),
-  "../plots/matrix/hierCluster.js": () => import("./hierCluster-KNPWL5KD.js"),
-  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-YGX6MZZW.js"),
-  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-5RTZUJVN.js"),
-  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-RH4BOM5F.js"),
-  "../plots/matrix/matrix.config.js": () => import("./matrix.config-RMDDMOZ5.js"),
-  "../plots/matrix/matrix.data.js": () => import("./matrix.data-Y5TPRGMW.js"),
-  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-Q5XSAUUH.js"),
-  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-6DXCAY4P.js"),
-  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-MGOYEKDN.js"),
-  "../plots/matrix/matrix.js": () => import("./matrix-XTKRVPMQ.js"),
-  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-T7EC5ZC2.js"),
-  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-S3E76TVO.js"),
-  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-GR77V3RL.js"),
-  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-3UGLZW25.js"),
-  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-A7CNLDUJ.js"),
-  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-6PZR3YOD.js"),
-  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-ZM7K7WI4.js"),
-  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-2DVRXVNH.js"),
-  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-YUCV7G5L.js"),
-  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-FESIQ2RC.js"),
-  "../plots/matrix/test/matrix.unit.spec.js": () => import("./matrix.unit.spec-6QF3WKM7.js"),
-  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-MUOKKCJN.js"),
-  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-YUDBYKX5.js"),
-  "../plots/plot.disco.js": () => import("./plot.disco-LV7RE3YO.js"),
-  "../plots/plot.ssgq.js": () => import("./plot.ssgq-F2LOQFYD.js"),
-  "../plots/singleCellPlot.js": () => import("./singleCellPlot-NDGIW32L.js"),
-  "../plots/stattable.js": () => import("./stattable-JBJVVLQE.js"),
-  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-WN36VUHL.js"),
-  "../plots/table.js": () => import("./table-EI2OIRGE.js"),
-  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-2NJ7JVJW.js"),
-  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-OOEU6WNB.js"),
-  "../plots/volcano/test/testData.js": () => import("./testData-DRM5HWQB.js")
-});
-
-// plots/importPlot.js
-async function importPlot(chartType, notFoundMessage = "") {
-  switch (chartType) {
-    case "aggMatrixInput":
-      return await import("./AggMatrixInput-GBQD74NV.js");
-    case "aggregateMatrix":
-      return await import("./AggregateMatrix-U2MOQOSZ.js");
-    case "animatedBubbleChart":
-      return await import("./animatedBubbleChart-GM2GXDP3.js");
-    case "brainImaging":
-      return await import("./brainImaging-OQB2ZHCU.js");
-    case "brainRegions":
-      return await import("./brainRegions-2CRVMS24.js");
-    case "barchart":
-      return await import("./barchart-EAXXILCH.js");
-    case "boxplot":
-      return await import("./BoxPlot-ZK6Q5JGE.js");
-    case "bubbleHeatmap":
-      return await import("./bubbleHeatmap-MANNFEG2.js");
-    case "cellTypeBubbleHeatmap":
-      return await import("./cellTypeBubbleHeatmap-LRK4R4EC.js");
-    case "correlationVolcano":
-      return await import("./CorrelationVolcano-WGR4JIGK.js");
-    case "cuminc":
-      return await import("./Cuminc-I6D6YSIL.js");
-    case "dataDownload":
-      return await import("./dataDownload-ZMAJUKBX.js");
-    case "DEinput":
-      return await import("./DEinput-6LX4I65N.js");
-    case "dictionary":
-      return await import("./dictionary-TQUVCHIN.js");
-    case "differentialAnalysis":
-      return await import("./DifferentialAnalysis-L5VVBCVZ.js");
-    case "Disco":
-      return await import("./Disco-HLARIYXU.js");
-    case "dmr":
-      return await import("./DmrPlot-BKQOT4JM.js");
-    case "facet":
-      return await import("./facet-RWQFAVVU.js");
-    case "GeneExpInput":
-      return await import("./GeneExpInput-APLFNE6N.js");
-    case "geneRanking":
-      return await import("./geneRanking-LV6W6TT7.js");
-    case "genomeBrowser":
-      return await import("./GB-WKFGDJYW.js");
-    case "geomap":
-      return await import("./Geomap-FTKWCV4J.js");
-    case "grin2":
-      return await import("./grin2-OXRU465E.js");
-    case "gsea":
-      return await import("./GSEA-DCCJI5JE.js");
-    case "imagePlot":
-      return await import("./imagePlot-OLVI26S5.js");
-    case "numericDictTermCluster":
-      return await import("./numericDictTermCluster-6XDVVWLE.js");
-    case "profileBarchart2":
-      return await import("./barchart2-E6A4UMUB.js");
-    case "profileForms":
-      return await import("./profileForms-BKP3OBKV.js");
-    case "profilePlot":
-      return await import("./profilePlot-5PRRNUKD.js");
-    case "profilePolar2":
-      return await import("./polar2-BGJA2GHZ.js");
-    case "profileRadar2":
-      return await import("./radar2-6BBT2FBT.js");
-    case "profileRadarFacility2":
-      return await import("./radarFacility2-76Q3IYP2.js");
-    case "proteinView":
-      return await import("./proteinView-VZIWIZZY.js");
-    case "proteomeAbundance":
-      return await import("./proteomeAbundance-NH3Y4YC7.js");
-    case "proteomeCohortCompare":
-      return await import("./proteomeCohortCompare-XZI5OI4X.js");
-    case "ProteomeInput":
-      return await import("./ProteomeInput-ZOBJ2VU6.js");
-    case "regression":
-      return await import("./Regression-ABKJOOMQ.js");
-    case "report":
-      return await import("./report-KB4K7ZXC.js");
-    case "runChart2":
-    //See frequencyChart
-    case "frequencyChart":
-      return await import("./RunChart2-D5CEEFEE.js");
-    case "sampleView":
-      return await import("./sampleView-QD2JLZ4T.js");
-    case "sampleScatter":
-      return await import("./scatter-OWFYLMSJ.js");
-    case "sc":
-      return await import("./SC-RLVEECU5.js");
-    case "studyCatalog":
-      return await import("./studyCatalog-NEL7XSIP.js");
-    case "cohortSunburst":
-      return await import("./cohortSunburst-KSTVS3OQ.js");
-    case "summarizeCnvGeneexp":
-      return await import("./summarizeCnvGeneexp-BZSCTA5W.js");
-    case "summarizeGeneexpSurvival":
-      return await import("./summarizeGeneexpSurvival-743KXNV7.js");
-    case "summarizeMutationDiagnosis":
-      return await import("./summarizeMutationDiagnosis-OTE7O4AS.js");
-    case "summarizeMutationSurvival":
-      return await import("./summarizeMutationSurvival-VOZOFTFM.js");
-    case "summarizeMutationCnv":
-      return await import("./summarizeMutationCnv-CALMSQGV.js");
-    case "summaryInput":
-      return await import("./summaryInput-JSOXVSMY.js");
-    case "summary":
-      return await import("./summary-XJKCD35N.js");
-    case "sunburst":
-      return await import("./sunburst-J3QHMYKW.js");
-    case "swimmer":
-      return await import("./swimmer-Z6FUH4CD.js");
-    case "survival":
-      return await import("./survival-FW7N3YXZ.js");
-    case "table":
-      return await import("./table-EI2OIRGE.js");
-    case "violin":
-      return await import("./Violin-PCNX2CWV.js");
-    case "volcano":
-      return await import("./Volcano-NVFNO7NE.js");
-    case "wsi":
-      return await import("./Wsi-MAMCK5YZ.js");
-    default:
-      if (notFoundMessage) throw notFoundMessage;
-      return await globImport_plots_js(`../plots/${chartType}.js`);
-  }
-}
-
-export {
-  importPlot
-};
-//# sourceMappingURL=chunk-YR6EXI2K.js.map

package/dist/chunk-Z53VY5JV.js

@@ -1,296 +0,0 @@
-import {
-  getSortOptions
-} from "./chunk-5DI4UNH5.js";
-import {
-  defaultUiLabels,
-  fillTermWrapper
-} from "./chunk-PEKCVKJK.js";
-import {
-  isDictionaryType
-} from "./chunk-JHLF2ZC2.js";
-import {
-  CNVClasses,
-  dtcnv,
-  mclass,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-WJLRU5OF.js";
-import {
-  copyMerge
-} from "./chunk-HBNB5TRH.js";
-
-// plots/matrix/matrix.config.js
-async function getPlotConfig(opts = {}, app) {
-  const controlLabels = structuredClone(defaultUiLabels);
-  const devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio;
-  const config = {
-    // data configuration
-    termgroups: [],
-    samplegroups: [],
-    divideBy: null,
-    legendValueFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    legendGrpFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    filter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    // cnvCutoffs: {},
-    // rendering options
-    settings: {
-      matrix: {
-        svgCanvasSwitch: 1e3,
-        // the number of samples to trigger switching between svg and canvas
-        useMinPixelWidth: true,
-        // canvas may be hazy if false, but more accurately reflects column density
-        cellEncoding: "",
-        // can be "oncoprint" | "stacked" | "single"
-        margin: {
-          top: 10,
-          right: 5,
-          bottom: 20,
-          left: 50
-        },
-        // set any dataset-defined sample limits and sort priority, otherwise undefined
-        // put in settings, so that later may be overridden by a user
-        maxGenes: opts.settings?.maxGenes || 50,
-        maxSample: opts.settings?.maxSample || 1e3,
-        sampleNameFilter: "",
-        sortSamplesBy: "a",
-        sortPriority: void 0,
-        // will be filled-in
-        sortBySampleAncestry: app.vocabApi.termdbConfig.hasSampleAncestry ? "last" : false,
-        // indicates sorting priority by sample ancestry
-        mapChildren2Root: false,
-        // for a dataset with sample ancestry, show one column per root sample (e.g. patient)
-        // sortByMutation: 'consequence', computed
-        // sortByCNV: true, computed
-        //sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),
-        sortSampleGrpsBy: "name",
-        // 'hits' | 'name' | 'sampleCount'
-        sortSamplesTieBreakers: [{
-          $id: "sample",
-          sortSamples: {}
-          /*split: {char: '', index: 0}*/
-        }],
-        sortTermsBy: "sampleCount",
-        // or 'as listed'
-        // do not show number of samples at hiercluster gene row labels
-        samplecount4gene: opts.chartType == "hierCluster" ? "" : "abs",
-        //true, // 'abs' (default, previously true), 'pct', ''  (previously false)
-        geneVariantCountSamplesSkipMclass: [],
-        cellbg: "#ececec",
-        showGrid: "",
-        // false | 'pattern' | 'rect'
-        // whether to show these controls buttons
-        addMutationCNVButtons: false,
-        truncatingMutations,
-        proteinChangingMutations,
-        synonymousMutations,
-        mutationClasses,
-        CNVClasses,
-        gridStroke: "#fff",
-        outlineStroke: "#ccc",
-        beamStroke: "#f00",
-        colw: 0,
-        colwMin: 0.1 / devicePixelRatio,
-        colwMax: 16,
-        colspace: 1,
-        colgspace: 8,
-        colglabelpos: true,
-        collabelpos: "bottom",
-        collabelvisible: true,
-        collabelgap: 5,
-        collabelpad: 1,
-        collabelmaxchars: 32,
-        rowh: 18,
-        //use 0 to auto-compute row height, previous default=18,
-        rowhMin: 1,
-        rowhMax: 20,
-        rowspace: 1,
-        rowgspace: 8,
-        rowlabelpos: "left",
-        // | 'right'
-        rowlabelgap: 5,
-        rowlabelvisible: true,
-        rowlabelpad: 1,
-        rowlabelmaxchars: 32,
-        legendGrpLabelMaxChars: 26,
-        grpLabelFontSize: 12,
-        minLabelFontSize: 6,
-        maxLabelFontSize: 14,
-        transpose: false,
-        // 'auto' shows column labels only when columns are wide enough (colw >= minLabelFontSize);
-        sampleLabelsToggle: "auto",
-        // 'auto' | 'hide'
-        sampleLabelOffset: 120,
-        sampleGrpLabelOffset: 120,
-        sampleGrpLabelMaxChars: 32,
-        termLabelOffset: 80,
-        termGrpLabelOffset: 80,
-        termGrpLabelMaxChars: 32,
-        duration: 0,
-        zoomLevel: 1,
-        zoomCenterPct: 0,
-        zoomIndex: 0,
-        zoomGrpIndex: 0,
-        zoomMin: 0.5,
-        zoomIncrement: 0.1,
-        zoomStep: 1,
-        // renderedWMax should not be exposed as a user-input
-        // 60000 pixels is based on laptop and external monitor tests,
-        // when a canvas dataURL image in a zoomed-in matrix svg stops rendering
-        imgWMax: 6e4 / devicePixelRatio,
-        scrollHeight: 12,
-        controlLabels,
-        cnvUnit: "log2ratio",
-        ignoreCnvValues: false,
-        //will ignore numeric CNV values if true
-        barh: 32,
-        // default bar height for continuous terms,
-        // possible string entries:
-        // - "genesetEdit", for gene-centric embedders only like GDC OncoMatrix
-        // - may add other optional hints later
-        showHints: [],
-        genesetEditUiVersion: "",
-        // '' | 'withTabs'
-        // settings for a specific tw
-        twSpecificSettings: {},
-        oncoPrintSNVindelCellBorder: false,
-        // whether to show white cell border for SNVindel in oncoPrint mode
-        cnvValues: {
-          //Properties match the args for the ColorScales
-          //numericInput arg
-          cutoffMode: "percentile",
-          defaultPercentile: 99,
-          min: null,
-          max: null,
-          percentile: 99
-        }
-      }
-    }
-  };
-  const s = config.settings;
-  const fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12);
-  s.legend = {
-    ontop: false,
-    lineh: 25,
-    padx: 5,
-    padleft: 0,
-    //150,
-    padright: 20,
-    padbtm: 30,
-    fontsize,
-    iconh: fontsize - 2,
-    iconw: fontsize - 2,
-    hangleft: 1,
-    linesep: false
-  };
-  const overrides = app.vocabApi.termdbConfig.matrix || {};
-  copyMerge(config.settings.matrix, overrides.settings);
-  if (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter;
-  if (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter;
-  if (overrides.filter) config.filter = overrides.filter;
-  if (opts.name) {
-    const data = await app.vocabApi.getMatrixByName(opts.name);
-    if (!data) throw "error from getMatrixByName()";
-    if (data.error) throw data.error;
-    copyMerge(config, data);
-  }
-  const os = opts?.settings?.matrix;
-  if (os) {
-    if ((os.sortSamplesBy == "custom" || os.sortSamplesBy == "asListed") && os.sortOptions?.custom.label == "against alteration type") {
-      os.sortSamplesBy = "a";
-    }
-    if (os.sortOptions) {
-      delete os.sortOptions.custom;
-      delete os.sortOptions.asListed;
-    }
-  }
-  copyMerge(config, opts);
-  const m = config.settings.matrix;
-  m.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m);
-  m.duration = 0;
-  m.colw = 0;
-  if (m.sortSamplesBy != "asListed" && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = "a";
-  else if (["selectedTerms", "class", "dt", "hits"].includes(m.sortSamplesBy)) m.sortSamplesBy = "a";
-  if (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = "abs";
-  if (window.location.hostname == "localhost") {
-    if (window.location.hash == "#canvas") m.svgCanvasSwitch = 0;
-  }
-  for (const grp of config.termgroups) {
-    const promises = [];
-    for (const tw of grp.lst) {
-      if (!tw.term?.type || isDictionaryType(tw.term.type)) {
-        if (!tw.id && tw.term.type != "samplelst" && tw.term.type != "termCollection") {
-          if (!tw.term.id) throw `missing tw.id and tw.term.id`;
-          tw.id = tw.term.id;
-        }
-        if (tw.term?.type != "samplelst" && tw.term?.type != "termCollection") delete tw.term;
-      }
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    grp.lst = await Promise.all(promises);
-  }
-  if (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi);
-  return config;
-}
-function setComputedConfig(config) {
-  const s = config.settings.matrix;
-  const allClasses = [...s.mutationClasses, ...s.CNVClasses];
-  s.filterByClass = { isAtomic: true };
-  for (const f of config.legendGrpFilter.lst) {
-    if (!f.dt) continue;
-    allClasses.filter((m) => f.dt.includes(mclass[m].dt)).forEach((key2) => {
-      s.filterByClass[key2] = "value";
-    });
-  }
-  for (const f of config.legendValueFilter.lst) {
-    if (!f.legendGrpName || f.tvs?.term?.type !== "geneVariant") continue;
-    if (f.tvs.values?.[0].mclasslst)
-      f.tvs.values[0].mclasslst.forEach((key2) => {
-        s.filterByClass[key2] = f.legendFilterType?.endsWith("_hard") ? "case" : "value";
-      });
-    else if (f.tvs.values)
-      f.tvs.values.forEach((v) => {
-        s.filterByClass[key] = "value";
-      });
-    else throw `unhandled tvs from legendValueFilter`;
-  }
-  s.hiddenVariants = Object.keys(s.filterByClass).filter((c) => c !== "isAtomic");
-  const hiddenCNVs = new Set(s.hiddenVariants.filter((key2) => mclass[key2]?.dt === dtcnv));
-  s.hiddenCNVs = [...hiddenCNVs];
-  s.showMatrixCNV = !hiddenCNVs.size ? "all" : hiddenCNVs.size == s.CNVClasses.length ? "none" : "bySelection";
-  s.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length;
-  const hiddenMutations = new Set(s.hiddenVariants.filter((key2) => s.mutationClasses.find((k) => k === key2)));
-  s.hiddenMutations = [...hiddenMutations];
-  const PCset = new Set(s.proteinChangingMutations);
-  const TMset = new Set(s.truncatingMutations);
-  s.showMatrixMutation = !hiddenMutations.size ? "all" : hiddenMutations.size == s.mutationClasses.length ? "none" : hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every((m) => !PCset.has(m)) ? "onlyPC" : hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every((m) => !TMset.has(m)) ? "onlyTruncating" : "bySelection";
-  s.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length;
-  const tiebreakers = s.sortOptions.a?.sortPriority.find((sp) => sp.types.length == 1 && sp.types[0] == "geneVariant")?.tiebreakers || [];
-  s.sortByMutation = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 1)?.isOrdered ? "consequence" : "presence";
-  s.sortByCNV = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 4)?.disabled !== true;
-}
-
-export {
-  getPlotConfig,
-  setComputedConfig
-};
-//# sourceMappingURL=chunk-Z53VY5JV.js.map