@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/chunk-ZTJLENGZ.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 devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio\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\t// cnvCutoffs: {},\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 / 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\t// 'auto' shows column labels only when columns are wide enough (colw >= minLabelFontSize);\n\t\t\t\tsampleLabelsToggle: 'auto', // 'auto' | 'hide'\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 / 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\tgenesetEditUiVersion: '', // '' | 'withTabs'\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\tcnvValues: {\n\t\t\t\t\t//Properties match the args for the ColorScales\n\t\t\t\t\t//numericInput arg\n\t\t\t\t\tcutoffMode: 'percentile',\n\t\t\t\t\tdefaultPercentile: 99,\n\t\t\t\t\tmin: null,\n\t\t\t\t\tmax: null,\n\t\t\t\t\tpercentile: 99\n\t\t\t\t}\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\t/** If tw fails at this step, consider using structuredClone(tw) in\n\t\t\t * the config for app.dispatch() to make the tw mutable. Should\n\t\t\t * not fail from runpp(), only app.dispatch(). */\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? 'all'\n\t\t: hiddenMutations.size == s.mutationClasses.length\n\t\t? 'none'\n\t\t: hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every(m => !PCset.has(m))\n\t\t? 'onlyPC'\n\t\t: hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every(m => !TMset.has(m))\n\t\t? 'onlyTruncating'\n\t\t: 'bySelection'\n\ts.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length\n\n\tconst tiebreakers =\n\t\ts.sortOptions.a?.sortPriority.find(sp => sp.types.length == 1 && sp.types[0] == 'geneVariant')?.tiebreakers || []\n\n\t//Backwards compatibility fix for old saved sessions missing .isOrdered and/or .disabled\n\ts.sortByMutation = tiebreakers.find(tb => tb.filter?.values[0]?.dt === 1)?.isOrdered ? 'consequence' : 'presence'\n\n\ts.sortByCNV = tiebreakers.find(tb => tb.filter?.values[0]?.dt === 4)?.disabled !== true\n}\n"],
+  "mappings": 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+  "names": ["key"]
+}

package/dist/condition-6UUQ3AAI.js

@@ -0,0 +1,332 @@
+import {
+  getPillNameDefault,
+  make_radios,
+  sayerror,
+  set_hiddenvalues,
+  throwMsgWithFilePathAndFnName
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// termsetting/handlers/condition.ts
+var cutoffGrades = [1, 2, 3, 4, 5];
+function getHandler(self) {
+  return {
+    getPillName(d) {
+      return getPillNameDefault(self, d);
+    },
+    getPillStatus() {
+      return getPillStatus(self);
+    },
+    showEditMenu(div) {
+      if (self.q.mode == "discrete") {
+        return showMenu_discrete(self, div);
+      }
+      if (self.q.mode == "binary" || self.q.mode == "cuminc" || self.q.mode == "cox") {
+        return showMenu_cutoff(self, div);
+      }
+      console.error("invalid q.mode:", self.q.mode);
+      throw "invalid q.mode";
+    }
+    // async postMain() {
+    // 	const body = self.opts.getBodyParams?.() || {} //make sure term1_q is added
+    // 	const data = await self.vocabApi.getCategories(self.term, self.filter!, body)
+    // 	//not really sure this is necessary but it's consistent across other handlers
+    // 	self.category2samplecount = []
+    // 	for (const d of data.lst) {
+    // 		self.category2samplecount.push({
+    // 			key: d.key,
+    // 			label: d.label,
+    // 			count: d.samplecount
+    // 		})
+    // 		// }
+    // 	}
+    // }
+  };
+}
+function getPillStatus(self) {
+  const text = self.q?.name || self.q?.reuseId;
+  if (text) return { text };
+  if (self.q.mode == "discrete") {
+    if (self.q.breaks?.length) {
+      return { text: self.q.breaks.length + 1 + " groups" };
+    } else {
+      if (self.q.bar_by_grade) {
+        if (self.q.value_by_max_grade) return { text: "Max. Grade" };
+        if (self.q.value_by_most_recent) return { text: "Most Recent Grade" };
+        if (self.q.value_by_computable_grade) return { text: "Any Grade" };
+        return { text: "Error: unknown grade setting", bgcolor: "red" };
+      }
+      if (self.q.bar_by_children) return { text: "Sub-condition" };
+    }
+  }
+  if (self.q.mode == "binary") {
+    return {
+      text: self.usecase?.target == "regression" ? self.data.q.groups.find((x) => x.name != self.data.refGrp).name : "binary"
+    };
+  }
+  if (self.q.mode == "cuminc" || self.q.mode == "cox") {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    return { text: `Grades ${self.q.breaks[0]}-5` };
+  }
+  return {};
+}
+async function showMenu_discrete(self, div) {
+  const value_type_div = div.append("div").style("margin", "10px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  value_type_div.append("div").style("display", "inline-block").style("margin", "0px 0px 5px 5px").style("color", "rgb(136, 136, 136)").text("Grade type:");
+  const value_type_select = value_type_div.append("select").style("display", "inline").style("margin", "0px 10px").on("change", () => {
+    const i = value_type_select.property("selectedIndex");
+    self.q.bar_by_grade = i != 3;
+    self.q.bar_by_children = i == 3;
+    self.q.value_by_max_grade = i == 0;
+    self.q.value_by_most_recent = i == 1;
+    self.q.value_by_computable_grade = i == 2 || i == 3;
+    self.dom.tip.hide();
+    self.api.runCallback();
+  });
+  value_type_select.append("option").text("Max grade per patient");
+  value_type_select.append("option").text("Most recent grade per patient");
+  value_type_select.append("option").text("Any grade per patient");
+  if (self.term.subconditions) {
+    value_type_select.append("option").text("Sub-conditions");
+  }
+  value_type_select.property(
+    "selectedIndex",
+    self.q.bar_by_children ? 3 : self.q.value_by_computable_grade ? 2 : self.q.value_by_most_recent ? 1 : 0
+  );
+  if (self.q.bar_by_children) {
+    return;
+  }
+  const breaksSelectorDiv = div.append("div").style("margin", "20px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  breaksSelectorDiv.append("div").text("Divide grades into groups (optional):").style("margin", "0px 0px 10px 5px").style("color", "rgb(136, 136, 136)");
+  const holder = breaksSelectorDiv.append("div").style("display", "flex").style("align-items", "start").style("margin-left", "10px").style("width", "100%");
+  const gradeValuesDiv = holder.append("div").style("margin-right", "20px");
+  const rangeNameDiv = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center").style("margin-right", "5px");
+  gradeValuesDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Cutoff grades");
+  const textarea = gradeValuesDiv.append("textarea").style("width", "100px").style("height", "70px").on("keyup", textarea2gradeUI);
+  gradeValuesDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
+  if (self.q.breaks?.length) {
+    textarea.property("value", self.q.breaks.join("\n"));
+  }
+  textarea2gradeUI();
+  function textarea2gradeUI() {
+    rangeNameDiv.selectAll("*").remove();
+    const breaks = textarea2breaks();
+    if (!breaks.length) {
+      delete self.q.breaks;
+      delete self.q.groups;
+      return;
+    }
+    if (!self.term.values) throwMsgWithFilePathAndFnName(`Missing term values`);
+    const grades = Object.keys(self.term.values).filter((g) => !self.term.values?.[g].uncomputable).map(Number).sort((a, b) => a - b);
+    const groups = getGroups(grades, breaks);
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Label");
+    for (const [i, g] of groups.entries()) {
+      rangeNameDiv.append("div").text(g.name.replace(/Grades* /, ""));
+      rangeNameDiv.append("div").append("input").attr("type", "text").property("value", g.name).style("margin", "2px 0px").on("change", function() {
+        groups[i].name = this.value;
+      });
+    }
+    self.q.breaks = breaks;
+    self.q.groups = groups;
+  }
+  function textarea2breaks() {
+    const str = textarea.property("value").trim();
+    if (!str) return [];
+    const lst = [...new Set(str.split("\n"))];
+    const breaks = [];
+    for (const x of lst) {
+      const b = Number(x);
+      if (!Number.isInteger(b)) {
+        sayerror(div, "cutoff grade must be an integer value");
+        return [];
+      }
+      if (b < 1 || b > 5) {
+        sayerror(div, `cutoff grade must be within grades 1-5`);
+        return [];
+      }
+      breaks.push(b);
+    }
+    if (!breaks.length) return [];
+    return breaks.sort((i, j) => i - j);
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function showMenu_cutoff(self, div) {
+  const holder = div.append("div").style("margin", "10px").style("display", "grid").style("grid-template-columns", "auto auto").style("gap", "20px");
+  holder.append("div").text("Grade cutoff").style("opacity", 0.4);
+  const sd = holder.append("div");
+  const gradeSelect = sd.append("select").on("change", changeGradeSelect);
+  for (const i of cutoffGrades) {
+    gradeSelect.append("option").text(self.term.values?.[i].label);
+  }
+  gradeSelect.property("selectedIndex", self.q.breaks[0] - 1);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 1" : "Censored").style("opacity", 0.4);
+  const g1n = holder.append("div").style("opacity", 0.4);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 2" : "Event").style("opacity", 0.4);
+  const g2n = holder.append("div").style("opacity", 0.4);
+  changeGradeSelect();
+  function changeGradeSelect() {
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    g1n.selectAll("*").remove();
+    g2n.selectAll("*").remove();
+    const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+    for (const i of grades) {
+      if (i < grade) {
+        g1n.append("div").text(self.term.values?.[i].label);
+      } else {
+        g2n.append("div").text(self.term.values?.[i].label);
+      }
+    }
+  }
+  const timeUnit = self.vocabApi.termdbConfig.timeUnit;
+  let timeScaleChoice;
+  if (self.q.mode == "cox") {
+    timeScaleChoice = self.q.timeScale;
+    holder.append("div").text("Time axis").style("opacity", 0.4);
+    const options = [
+      {
+        label: timeUnit.charAt(0).toUpperCase() + timeUnit.slice(1),
+        value: "time"
+      },
+      { label: "Age", value: "age" }
+    ];
+    if (self.q.timeScale == "age") {
+      options[1].checked = true;
+    } else {
+      options[0].checked = true;
+    }
+    make_radios({
+      holder: holder.append("div"),
+      options,
+      styles: { padding: "" },
+      callback: (v) => timeScaleChoice = v
+    });
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    self.q.breaks[0] = grade;
+    if (self.q.mode == "binary") {
+      const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+      self.q.groups = getGroups(grades, self.q.breaks);
+      self.refGrp = self.q.groups[0].name;
+    }
+    if (self.q.mode == "cox") self.q.timeScale = timeScaleChoice;
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function getGroups(grades, breaks) {
+  grades.sort((a, b2) => a - b2);
+  const groups = [];
+  let group = { values: [] };
+  let b;
+  for (const g of grades) {
+    if (breaks.includes(g)) {
+      b = g;
+      const max = Math.max(...group.values);
+      if (!groups.length) {
+        if (group.values.length == 1) {
+          if (group.values[0] !== 0) throw "unexpected group value";
+          group.name = "Grade 0";
+        } else {
+          if (group.values.length == 2 && group.values.includes(-1) && group.values.includes(0)) {
+            group.name = "Not tested/Grade 0";
+          } else {
+            group.name = group.values.includes(-1) ? `Not tested/Grade 0 - Grade ${max}` : `Grades 0-${max}`;
+          }
+        }
+      } else {
+        group.name = group.values.length == 1 ? `Grade ${group.values[0]}` : `${group.name}-${max}`;
+      }
+      groups.push(group);
+      group = {
+        name: `Grade ${b}`,
+        values: [g]
+      };
+    } else {
+      group.values.push(g);
+    }
+  }
+  group.name = `Grades ${b}-5`;
+  groups.push(group);
+  return groups;
+}
+function fillTW(tw, vocabApi, defaultQ) {
+  set_hiddenvalues(tw.q, tw.term);
+  if (defaultQ) {
+    copyMerge(tw.q, defaultQ);
+  }
+  if (!Object.keys(tw.q).includes("mode")) tw.q.mode = "discrete";
+  if (!tw.q.valueFor) {
+    const q = tw.q;
+    if (!q.bar_by_grade && !q.bar_by_children) q.bar_by_grade = true;
+    tw.q.valueFor = tw.q.bar_by_children ? "children" : "grade";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.value_by_max_grade || tw.q.value_by_most_recent || tw.q.value_by_computable_grade) {
+    } else {
+      tw.q.value_by_max_grade = true;
+    }
+  }
+  if (tw.q.mode == "binary" || tw.q.mode == "cox" || tw.q.mode == "cuminc") {
+    const defaultBreak = tw.q.mode == "binary" ? 1 : 3;
+    if (!tw.q.breaks?.length) tw.q.breaks = [defaultBreak];
+    if (tw.q.breaks.length != 1 || ![1, 2, 3, 4, 5].includes(tw.q.breaks[0])) throw "invalid tw.q.breaks";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.breaks?.length) {
+      if (!tw.term.values) throw "missing term.values";
+      if (tw.q.mode == "discrete" || tw.q.mode == "binary") {
+        const grades = Object.keys(tw.term.values).filter((g) => tw.q.mode == "discrete" ? !tw.term.values?.[g].uncomputable : g).map(Number).sort((a, b) => a - b);
+        tw.q.groups = getGroups(grades, tw.q.breaks);
+      }
+    }
+    if (tw.q.mode == "cox") {
+      if (!tw.q.timeScale) tw.q.timeScale = "time";
+      if (!["age", "time"].includes(tw.q.timeScale)) throw "invalid q.timeScale";
+    }
+  }
+}
+export {
+  fillTW,
+  getHandler
+};
+//# sourceMappingURL=condition-6UUQ3AAI.js.map

package/dist/controls-N2NIGPHY.js

@@ -0,0 +1,41 @@
+import {
+  controlsInit,
+  renderTerm1Label,
+  term0_term2_defaultQ
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  controlsInit,
+  renderTerm1Label,
+  term0_term2_defaultQ
+};
+//# sourceMappingURL=controls-N2NIGPHY.js.map

package/dist/controls.config-YYIMJHWN.js

@@ -0,0 +1,39 @@
+import {
+  configUiInit,
+  initByInput
+} from "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  configUiInit,
+  initByInput
+};
+//# sourceMappingURL=controls.config-YYIMJHWN.js.map

package/dist/correlation-DYUMFMTU.js

@@ -0,0 +1,102 @@
+import {
+  appInit
+} from "./chunk-YIFCXFWE.js";
+import "./chunk-YRXB3MKU.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-B3XMNPZY.js";
+import "./chunk-VO4FCZOR.js";
+import "./chunk-GPGCGFFS.js";
+import "./chunk-34VSTY2U.js";
+import "./chunk-PJM6MUTT.js";
+import "./chunk-4KY4XKJV.js";
+import "./chunk-3LYZMOLO.js";
+import "./chunk-5QTJUPFS.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-LYULXXGR.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-CPMOBFFR.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-B4VBTVVQ.js";
+import "./chunk-IQTEW3SK.js";
+import "./chunk-MNPTPENH.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-UAALI7MC.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// gdc/correlation.ts
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  if (!genomes[useGenome]) throw useGenome + " missing";
+  const massApi = await appInit({
+    //debug: arg.debugmode, // is debug accepted?
+    genome: genomes[useGenome],
+    holder,
+    state: {
+      genome: useGenome,
+      dslabel: useDslabel,
+      termfilter: { filter0: arg.filter0 },
+      nav: { activeTab: 1, header_mode: window.location.pathname.includes("example.gdc") ? void 0 : "only_buttons" },
+      plots: arg.state?.plots || [
+        { chartType: "summaryInput" }
+        // default shows summaryInput ui, can change
+        //{ chartType: 'barchart', term: {id: 'case.demographic.gender'} }, // uncomment for quicker testing
+      ]
+    },
+    opts: Object.assign(
+      {
+        // todo additional customizations
+        // dictionary:{header:'Select a variable to build Correlation Plot'}
+        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
+      },
+      arg.opts || {}
+    ),
+    barchart: arg.opts?.barchart || {},
+    violin: arg.opts?.violin || {},
+    boxplot: arg.opts?.boxplot || {},
+    app: arg.opts?.app || {}
+  });
+  const api = {
+    update: async (updateArg) => {
+      if (!massApi) return;
+      if ("filter0" in updateArg) {
+        massApi.dispatch({
+          type: "app_refresh",
+          subactions: [
+            {
+              type: "filter_replace",
+              filter0: updateArg.filter0
+            }
+          ]
+        });
+      }
+    },
+    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
+  };
+  return api;
+}
+export {
+  init
+};
+//# sourceMappingURL=correlation-DYUMFMTU.js.map