@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

package/dist/chunk-FN5XPUPH.js

@@ -0,0 +1,83 @@
+// plots/bars.settings.js
+var plotLength = 300;
+var rendererSettings = JSON.stringify({
+  plotLength,
+  // maximum bar length
+  barwidth: 20,
+  // bar thickness
+  barspace: 2,
+  // space between two bars
+  orientation: "horizontal",
+  // vertical | horizontal
+  h: {},
+  relayTiles: false,
+  svgw: 600,
+  svgh: 400,
+  unit: "abs",
+  // abs | pct
+  scale: "byChart",
+  // byGroup | byChart
+  currAge: 20,
+  rowkey: "dataId",
+  rowgrpkey: "rowgrp",
+  colkey: "seriesId",
+  colgrpkey: "colgrp",
+  rowh: 22,
+  colw: 36,
+  rowspace: 1,
+  colspace: 1,
+  rowtick: 8,
+  coltick: 5,
+  rowlabtickspace: 0,
+  collabtickspace: 0,
+  collabelh: 100,
+  rowlabelw: 100,
+  rowheadleft: true,
+  colheadtop: false,
+  legendontop: false,
+  legendh: 0,
+  legendpadleft: 170,
+  hidelegend: false,
+  showgrid: true,
+  gridstroke: "#fff",
+  showEmptyCells: false,
+  cellbg: "#eeeeee",
+  fontsizeratio: 0.9,
+  rowlabelfontsizemax: 16,
+  collabelfontsizemax: 12,
+  crudefill: true,
+  duration: 1e3,
+  delay: 0,
+  cellfontsize: 11,
+  colgspace: 4,
+  rowgspace: 4,
+  rowglabspace: 5,
+  colglabspace: 5,
+  colgrplabelh: 25,
+  rowgrplabelw: 25,
+  rowglabfontsize: 15,
+  rowglabfontsizemax: 25,
+  colglabfontsize: 15,
+  colglabfontsizemax: 25,
+  borderwidth: 2,
+  svgPadding: {
+    top: 10,
+    left: 30,
+    right: 10,
+    bottom: 30
+  },
+  exclude: {
+    rows: [],
+    cols: [],
+    colgrps: [],
+    // used when expanding a column group
+    rowgrps: []
+  },
+  axisTitleFontSize: 16
+});
+
+export {
+  plotLength,
+  rendererSettings
+};
+//# sourceMappingURL=chunk-FN5XPUPH.js.map

package/dist/chunk-FN5XPUPH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/bars.settings.js"],
+  "sourcesContent": ["export const plotLength = 300\n\n// Example barchart renderer settings\nexport const rendererSettings = JSON.stringify({\n\tplotLength: plotLength, // maximum bar length\n\tbarwidth: 20, // bar thickness\n\tbarspace: 2, // space between two bars\n\n\torientation: 'horizontal', // vertical | horizontal\n\th: {},\n\trelayTiles: false,\n\tsvgw: 600,\n\tsvgh: 400,\n\tunit: 'abs', // abs | pct\n\tscale: 'byChart', // byGroup | byChart\n\tcurrAge: 20,\n\n\trowkey: 'dataId',\n\trowgrpkey: 'rowgrp',\n\tcolkey: 'seriesId',\n\tcolgrpkey: 'colgrp',\n\n\trowh: 22,\n\tcolw: 36,\n\n\trowspace: 1,\n\tcolspace: 1,\n\n\trowtick: 8,\n\tcoltick: 5,\n\trowlabtickspace: 0,\n\tcollabtickspace: 0,\n\n\tcollabelh: 100,\n\trowlabelw: 100,\n\trowheadleft: true,\n\tcolheadtop: false,\n\n\tlegendontop: false,\n\tlegendh: 0,\n\tlegendpadleft: 170,\n\thidelegend: false,\n\n\tshowgrid: true,\n\tgridstroke: '#fff',\n\tshowEmptyCells: false,\n\n\tcellbg: '#eeeeee',\n\n\tfontsizeratio: 0.9,\n\trowlabelfontsizemax: 16,\n\tcollabelfontsizemax: 12,\n\tcrudefill: true,\n\tduration: 1000,\n\tdelay: 0,\n\n\tcellfontsize: 11,\n\n\tcolgspace: 4,\n\trowgspace: 4,\n\trowglabspace: 5,\n\n\tcolglabspace: 5,\n\tcolgrplabelh: 25,\n\trowgrplabelw: 25,\n\n\trowglabfontsize: 15,\n\trowglabfontsizemax: 25,\n\tcolglabfontsize: 15,\n\tcolglabfontsizemax: 25,\n\tborderwidth: 2,\n\n\tsvgPadding: {\n\t\ttop: 10,\n\t\tleft: 30,\n\t\tright: 10,\n\t\tbottom: 30\n\t},\n\n\texclude: {\n\t\trows: [],\n\t\tcols: [],\n\t\tcolgrps: [], // used when expanding a column group\n\t\trowgrps: []\n\t},\n\taxisTitleFontSize: 16\n})\n"],
+  "mappings": ";AAAO,IAAM,aAAa;AAGnB,IAAM,mBAAmB,KAAK,UAAU;AAAA,EAC9C;AAAA;AAAA,EACA,UAAU;AAAA;AAAA,EACV,UAAU;AAAA;AAAA,EAEV,aAAa;AAAA;AAAA,EACb,GAAG,CAAC;AAAA,EACJ,YAAY;AAAA,EACZ,MAAM;AAAA,EACN,MAAM;AAAA,EACN,MAAM;AAAA;AAAA,EACN,OAAO;AAAA;AAAA,EACP,SAAS;AAAA,EAET,QAAQ;AAAA,EACR,WAAW;AAAA,EACX,QAAQ;AAAA,EACR,WAAW;AAAA,EAEX,MAAM;AAAA,EACN,MAAM;AAAA,EAEN,UAAU;AAAA,EACV,UAAU;AAAA,EAEV,SAAS;AAAA,EACT,SAAS;AAAA,EACT,iBAAiB;AAAA,EACjB,iBAAiB;AAAA,EAEjB,WAAW;AAAA,EACX,WAAW;AAAA,EACX,aAAa;AAAA,EACb,YAAY;AAAA,EAEZ,aAAa;AAAA,EACb,SAAS;AAAA,EACT,eAAe;AAAA,EACf,YAAY;AAAA,EAEZ,UAAU;AAAA,EACV,YAAY;AAAA,EACZ,gBAAgB;AAAA,EAEhB,QAAQ;AAAA,EAER,eAAe;AAAA,EACf,qBAAqB;AAAA,EACrB,qBAAqB;AAAA,EACrB,WAAW;AAAA,EACX,UAAU;AAAA,EACV,OAAO;AAAA,EAEP,cAAc;AAAA,EAEd,WAAW;AAAA,EACX,WAAW;AAAA,EACX,cAAc;AAAA,EAEd,cAAc;AAAA,EACd,cAAc;AAAA,EACd,cAAc;AAAA,EAEd,iBAAiB;AAAA,EACjB,oBAAoB;AAAA,EACpB,iBAAiB;AAAA,EACjB,oBAAoB;AAAA,EACpB,aAAa;AAAA,EAEb,YAAY;AAAA,IACX,KAAK;AAAA,IACL,MAAM;AAAA,IACN,OAAO;AAAA,IACP,QAAQ;AAAA,EACT;AAAA,EAEA,SAAS;AAAA,IACR,MAAM,CAAC;AAAA,IACP,MAAM,CAAC;AAAA,IACP,SAAS,CAAC;AAAA;AAAA,IACV,SAAS,CAAC;AAAA,EACX;AAAA,EACA,mBAAmB;AACpB,CAAC;",
+  "names": []
+}

package/dist/chunk-FRLEROW5.js

@@ -0,0 +1,279 @@
+import {
+  getSortOptions
+} from "./chunk-B65X5UQH.js";
+import {
+  defaultUiLabels
+} from "./chunk-OA7TPCTX.js";
+import {
+  fillTermWrapper
+} from "./chunk-PX7A6LBY.js";
+import {
+  isDictionaryType
+} from "./chunk-DKI7YOTJ.js";
+import {
+  CNVClasses,
+  dtcnv,
+  mclass,
+  mutationClasses,
+  proteinChangingMutations,
+  synonymousMutations,
+  truncatingMutations
+} from "./chunk-6VQ4C735.js";
+import {
+  copyMerge
+} from "./chunk-DDOM4XYV.js";
+
+// plots/matrix/matrix.config.js
+async function getPlotConfig(opts = {}, app) {
+  const controlLabels = structuredClone(defaultUiLabels);
+  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
+        // 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 / window.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,
+        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 / window.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: [],
+        // settings for a specific tw
+        twSpecificSettings: {},
+        oncoPrintSNVindelCellBorder: false
+        // whether to show white cell border for SNVindel in oncoPrint mode
+      }
+    }
+  };
+  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-FRLEROW5.js.map

package/dist/chunk-FRLEROW5.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.config.js"],
+  "sourcesContent": ["import { copyMerge } from '#rx'\nimport { getSortOptions } from './matrix.sort'\nimport { fillTermWrapper } from '#termsetting'\nimport {\n\tmclass,\n\tdtcnv,\n\tproteinChangingMutations,\n\ttruncatingMutations,\n\tsynonymousMutations,\n\tmutationClasses,\n\tCNVClasses\n} from '#shared/common.js'\nimport { isDictionaryType } from '#shared/terms.js'\nimport { defaultUiLabels } from '#plots/PlotBase.js'\n\nexport async function getPlotConfig(opts = {}, app) {\n\tconst controlLabels = structuredClone(defaultUiLabels)\n\tconst config = {\n\t\t// data configuration\n\t\ttermgroups: [],\n\t\tsamplegroups: [],\n\t\tdivideBy: null,\n\t\tlegendValueFilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\tlegendGrpFilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\tfilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\tcnvCutoffs: {},\n\n\t\t// rendering options\n\t\tsettings: {\n\t\t\tmatrix: {\n\t\t\t\tsvgCanvasSwitch: 1000, // the number of samples to trigger switching between svg and canvas\n\t\t\t\tuseMinPixelWidth: true, // canvas may be hazy if false, but more accurately reflects column density\n\t\t\t\tcellEncoding: '', // can be \"oncoprint\" | \"stacked\" | \"single\"\n\t\t\t\tmargin: {\n\t\t\t\t\ttop: 10,\n\t\t\t\t\tright: 5,\n\t\t\t\t\tbottom: 20,\n\t\t\t\t\tleft: 50\n\t\t\t\t},\n\t\t\t\t// set any dataset-defined sample limits and sort priority, otherwise undefined\n\t\t\t\t// put in settings, so that later may be overridden by a user\n\t\t\t\tmaxGenes: opts.settings?.maxGenes || 50,\n\t\t\t\tmaxSample: opts.settings?.maxSample || 1000,\n\n\t\t\t\tsampleNameFilter: '',\n\t\t\t\tsortSamplesBy: 'a',\n\t\t\t\tsortPriority: undefined, // will be filled-in\n\t\t\t\t// sortByMutation: 'consequence', computed\n\t\t\t\t// sortByCNV: true, computed\n\t\t\t\t//sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),\n\t\t\t\tsortSampleGrpsBy: 'name', // 'hits' | 'name' | 'sampleCount'\n\t\t\t\tsortSamplesTieBreakers: [{ $id: 'sample', sortSamples: {} /*split: {char: '', index: 0}*/ }],\n\t\t\t\tsortTermsBy: 'sampleCount', // or 'as listed'\n\t\t\t\t// do not show number of samples at hiercluster gene row labels\n\t\t\t\tsamplecount4gene: opts.chartType == 'hierCluster' ? '' : 'abs', //true, // 'abs' (default, previously true), 'pct', ''  (previously false)\n\t\t\t\tgeneVariantCountSamplesSkipMclass: [],\n\t\t\t\tcellbg: '#ececec',\n\t\t\t\tshowGrid: '', // false | 'pattern' | 'rect'\n\t\t\t\t// whether to show these controls buttons\n\t\t\t\taddMutationCNVButtons: false,\n\t\t\t\ttruncatingMutations,\n\t\t\t\tproteinChangingMutations,\n\t\t\t\tsynonymousMutations,\n\t\t\t\tmutationClasses,\n\t\t\t\tCNVClasses,\n\t\t\t\tgridStroke: '#fff',\n\t\t\t\toutlineStroke: '#ccc',\n\t\t\t\tbeamStroke: '#f00',\n\t\t\t\tcolw: 0,\n\t\t\t\tcolwMin: 0.1 / window.devicePixelRatio,\n\t\t\t\tcolwMax: 16,\n\t\t\t\tcolspace: 1,\n\t\t\t\tcolgspace: 8,\n\t\t\t\tcolglabelpos: true,\n\t\t\t\tcollabelpos: 'bottom',\n\t\t\t\tcollabelvisible: true,\n\t\t\t\tcollabelgap: 5,\n\t\t\t\tcollabelpad: 1,\n\t\t\t\tcollabelmaxchars: 32,\n\t\t\t\trowh: 18, //use 0 to auto-compute row height, previous default=18,\n\t\t\t\trowhMin: 1,\n\t\t\t\trowhMax: 20,\n\t\t\t\trowspace: 1,\n\t\t\t\trowgspace: 8,\n\t\t\t\trowlabelpos: 'left', // | 'right'\n\t\t\t\trowlabelgap: 5,\n\t\t\t\trowlabelvisible: true,\n\t\t\t\trowlabelpad: 1,\n\t\t\t\trowlabelmaxchars: 32,\n\t\t\t\tlegendGrpLabelMaxChars: 26,\n\t\t\t\tgrpLabelFontSize: 12,\n\t\t\t\tminLabelFontSize: 6,\n\t\t\t\tmaxLabelFontSize: 14,\n\t\t\t\ttranspose: false,\n\t\t\t\tsampleLabelOffset: 120,\n\t\t\t\tsampleGrpLabelOffset: 120,\n\t\t\t\tsampleGrpLabelMaxChars: 32,\n\t\t\t\ttermLabelOffset: 80,\n\t\t\t\ttermGrpLabelOffset: 80,\n\t\t\t\ttermGrpLabelMaxChars: 32,\n\t\t\t\tduration: 0,\n\t\t\t\tzoomLevel: 1,\n\t\t\t\tzoomCenterPct: 0,\n\t\t\t\tzoomIndex: 0,\n\t\t\t\tzoomGrpIndex: 0,\n\t\t\t\tzoomMin: 0.5,\n\t\t\t\tzoomIncrement: 0.1,\n\t\t\t\tzoomStep: 1,\n\t\t\t\t// renderedWMax should not be exposed as a user-input\n\t\t\t\t// 60000 pixels is based on laptop and external monitor tests,\n\t\t\t\t// when a canvas dataURL image in a zoomed-in matrix svg stops rendering\n\t\t\t\timgWMax: 60000 / window.devicePixelRatio,\n\t\t\t\tscrollHeight: 12,\n\t\t\t\tcontrolLabels,\n\t\t\t\tcnvUnit: 'log2ratio',\n\t\t\t\tignoreCnvValues: false, //will ignore numeric CNV values if true\n\n\t\t\t\tbarh: 32, // default bar height for continuous terms,\n\n\t\t\t\t// possible string entries:\n\t\t\t\t// - \"genesetEdit\", for gene-centric embedders only like GDC OncoMatrix\n\t\t\t\t// - may add other optional hints later\n\t\t\t\tshowHints: [],\n\t\t\t\t// settings for a specific tw\n\t\t\t\ttwSpecificSettings: {},\n\t\t\t\toncoPrintSNVindelCellBorder: false // whether to show white cell border for SNVindel in oncoPrint mode\n\t\t\t}\n\t\t}\n\t}\n\n\tconst s = config.settings\n\tconst fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12)\n\n\ts.legend = {\n\t\tontop: false,\n\t\tlineh: 25,\n\t\tpadx: 5,\n\t\tpadleft: 0, //150,\n\t\tpadright: 20,\n\t\tpadbtm: 30,\n\t\tfontsize,\n\t\ticonh: fontsize - 2,\n\t\ticonw: fontsize - 2,\n\t\thangleft: 1,\n\t\tlinesep: false\n\t}\n\n\tconst overrides = app.vocabApi.termdbConfig.matrix || {}\n\tcopyMerge(config.settings.matrix, overrides.settings)\n\tif (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter\n\tif (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter\n\tif (overrides.filter) config.filter = overrides.filter\n\n\tif (opts.name) {\n\t\t// name should be identifier of a premade plot from the datase; load data of the premade plot and override into config{}\n\t\tconst data = await app.vocabApi.getMatrixByName(opts.name)\n\t\tif (!data) throw 'error from getMatrixByName()'\n\t\tif (data.error) throw data.error\n\t\tcopyMerge(config, data)\n\t}\n\n\tconst os = opts?.settings?.matrix\n\tif (os) {\n\t\tif (\n\t\t\t(os.sortSamplesBy == 'custom' || os.sortSamplesBy == 'asListed') &&\n\t\t\tos.sortOptions?.custom.label == 'against alteration type'\n\t\t) {\n\t\t\tos.sortSamplesBy = 'a'\n\t\t}\n\t\tif (os.sortOptions) {\n\t\t\tdelete os.sortOptions.custom\n\t\t\tdelete os.sortOptions.asListed\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\tcopyMerge(config, opts)\n\tconst m = config.settings.matrix\n\tm.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m)\n\t// harcode these overrides for now\n\tm.duration = 0\n\t// force auto-dimensions for colw\n\tm.colw = 0\n\t// support deprecated sortSamplesBy value from a saved session\n\tif (m.sortSamplesBy != 'asListed' && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = 'a'\n\telse if (['selectedTerms', 'class', 'dt', 'hits'].includes(m.sortSamplesBy)) m.sortSamplesBy = 'a'\n\tif (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = 'abs'\n\t// support overrides in localhost\n\tif (window.location.hostname == 'localhost') {\n\t\tif (window.location.hash == '#canvas') m.svgCanvasSwitch = 0\n\t}\n\n\tfor (const grp of config.termgroups) {\n\t\tconst promises = []\n\t\t//grp.lst = JSON.parse(JSON.stringify(grp.lst))\n\t\tfor (const tw of grp.lst) {\n\t\t\t// may force the saved session to request the most up-to-data dictionary term data from server\n\t\t\t// TODO: should skip samplelst term here\n\t\t\tif (!tw.term?.type || isDictionaryType(tw.term.type)) {\n\t\t\t\tif (!tw.id && tw.term.type != 'samplelst' && tw.term.type != 'termCollection') {\n\t\t\t\t\tif (!tw.term.id) throw `missing tw.id and tw.term.id`\n\t\t\t\t\ttw.id = tw.term.id // tw.id will be used to rehydrate tw with new term data from server. tw.id will be deleted following rehydration.\n\t\t\t\t}\n\t\t\t\tif (tw.term?.type != 'samplelst' && tw.term?.type != 'termCollection') delete tw.term\n\t\t\t}\n\t\t\tpromises.push(fillTermWrapper(tw, app.vocabApi))\n\t\t}\n\t\tgrp.lst = await Promise.all(promises)\n\t}\n\tif (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi)\n\treturn config\n}\n\n// config: a hydrated matrix config object\nexport function setComputedConfig(config) {\n\tconst s = config.settings.matrix\n\tconst allClasses = [...s.mutationClasses, ...s.CNVClasses]\n\n\ts.filterByClass = { isAtomic: true }\n\tfor (const f of config.legendGrpFilter.lst) {\n\t\tif (!f.dt) continue\n\t\tallClasses\n\t\t\t.filter(m => f.dt.includes(mclass[m].dt))\n\t\t\t.forEach(key => {\n\t\t\t\ts.filterByClass[key] = 'value'\n\t\t\t})\n\t}\n\tfor (const f of config.legendValueFilter.lst) {\n\t\tif (!f.legendGrpName || f.tvs?.term?.type !== 'geneVariant') continue\n\t\tif (f.tvs.values?.[0].mclasslst)\n\t\t\tf.tvs.values[0].mclasslst.forEach(key => {\n\t\t\t\ts.filterByClass[key] = f.legendFilterType?.endsWith('_hard') ? 'case' : 'value'\n\t\t\t})\n\t\telse if (f.tvs.values)\n\t\t\tf.tvs.values.forEach(v => {\n\t\t\t\t//hiddenVariants.add(v.key)\n\t\t\t\ts.filterByClass[key] = 'value'\n\t\t\t})\n\t\telse throw `unhandled tvs from legendValueFilter`\n\t}\n\ts.hiddenVariants = Object.keys(s.filterByClass).filter(c => c !== 'isAtomic')\n\n\tconst hiddenCNVs = new Set(s.hiddenVariants.filter(key => mclass[key]?.dt === dtcnv))\n\ts.hiddenCNVs = [...hiddenCNVs]\n\n\ts.showMatrixCNV = !hiddenCNVs.size ? 'all' : hiddenCNVs.size == s.CNVClasses.length ? 'none' : 'bySelection'\n\ts.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length\n\n\tconst hiddenMutations = new Set(s.hiddenVariants.filter(key => s.mutationClasses.find(k => k === key)))\n\ts.hiddenMutations = [...hiddenMutations]\n\tconst PCset = new Set(s.proteinChangingMutations)\n\tconst TMset = new Set(s.truncatingMutations)\n\n\ts.showMatrixMutation = !hiddenMutations.size\n\t\t? 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