@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-77ZJGPK2.js

@@ -0,0 +1,289 @@
+import {
+  getSortOptions
+} from "./chunk-5UMPBVA6.js";
+import {
+  defaultUiLabels,
+  fillTermWrapper
+} from "./chunk-OXJ2TWDO.js";
+import {
+  copyMerge
+} from "./chunk-MVTCBVSX.js";
+import {
+  isDictionaryType
+} from "./chunk-6ITDJ5UR.js";
+import {
+  CNVClasses,
+  dtcnv,
+  mclass,
+  mutationClasses,
+  proteinChangingMutations,
+  synonymousMutations,
+  truncatingMutations
+} from "./chunk-XYFDBYOY.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
+        // 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,
+        sampleLabelsToggle: opts.chartType === "hierCluster" ? "hide" : "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: [],
+        // 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-77ZJGPK2.js.map

package/dist/chunk-77ZJGPK2.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\tsampleLabelsToggle: opts.chartType === 'hierCluster' ? 'hide' : '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\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') ? 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+  "names": ["key"]
+}

package/dist/chunk-7FKIAQ4K.js

@@ -0,0 +1,17 @@
+// ../shared/types/src/routes/termdb.violinBox.ts
+function isErrorResponse(response) {
+  return "error" in response && "status" in response;
+}
+
+// ../shared/types/src/routes/samplewsimages.ts
+var WSImage = class {
+  constructor(filename) {
+    this.filename = filename;
+  }
+};
+
+export {
+  WSImage,
+  isErrorResponse
+};
+//# sourceMappingURL=chunk-7FKIAQ4K.js.map

package/dist/chunk-7FKIAQ4K.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/types/src/routes/termdb.violinBox.ts", "../../shared/types/src/routes/samplewsimages.ts"],
+  "sourcesContent": ["import type { RoutePayload } from './routeApi.js'\nimport type { TermWrapper } from '../terms/tw.ts'\nimport type { Filter } from '../filter.ts'\nimport type { ErrorResponse } from './errorResponse.ts'\nimport type { DescrStats } from './termdb.descrstats.ts'\n\n/** Common properties shared by both violin and box plots */\ntype CommonProps = {\n\t/** numeric tw to fetch numeric data. tw.q.mode must be continuous */\n\ttw: TermWrapper\n\tdslabel: string\n\tgenome: string\n\t/** overlay tw for multiple violins/boxplots */\n\toverlayTw?: TermWrapper\n\t/** tw to divide to multiple charts */\n\tdivideTw?: TermWrapper\n\t/** mass filter */\n\tfilter?: Filter\n\t/** read-only invisible filter */\n\tfilter0?: any\n\t/** TODO: Needs description FIXME delete */\n\tcurrentGeneNames?: string[]\n\t/** if true, use log scale; if false or undefined, use linear scale */\n\tisLogScale?: boolean\n}\n\n/** Request type for violin plots with required violin-specific parameters */\nexport type ViolinRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'violin'\n\t/** A number representing the dimension perpendicular to the violin spread */\n\taxisHeight?: number\n\t/** A string representing the type of symbol used on the plot */\n\tdatasymbol?: string\n\t/** A number representing the device's pixel ratio */\n\tdevicePixelRatio: number\n\t/** If true, uses KDE method to build plot */\n\tisKDE?: boolean\n\t/** A string with two possible values: 'horizontal' or 'vertical' */\n\torientation: string\n\t/** A number representing the radius of the data symbols */\n\tradius: number\n\t/** A number representing the right margin */\n\trightMargin?: number\n\t/** Term may be scaled from regression analysis */\n\tscale?: any\n\t/** A number representing the width of the stroke */\n\tstrokeWidth?: number\n\t/** A number representing the width of the SVG box */\n\tsvgw: number\n\t/** Number of bins to build the plot. Default is 20. */\n\tticks?: number\n}\n\n/** Request type for box plots with required box-specific parameters */\nexport type BoxRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'box'\n\t/** sort plots by median value */\n\torderByMedian?: boolean\n\t/** Remove outliers from the plot */\n\tremoveOutliers?: boolean\n\t/** If true, show association tests table */\n\tshowAssocTests?: boolean\n}\n\n/**Unified request type for violin and boxplot - union of ViolinRequest and BoxRequest */\nexport type ViolinBoxRequest = ViolinRequest | BoxRequest\n\nexport type ViolinBoxResponse = ViolinResponse | BoxPlotResponse | ErrorResponse\n\n/** Type guard to check if response is an ErrorResponse */\nexport function isErrorResponse(response: ViolinBoxResponse): response is ErrorResponse {\n\treturn 'error' in response && 'status' in response\n}\n\n/** Type guard to check if response is a BoxPlotResponse */\nexport function isBoxPlotResponse(response: ViolinBoxResponse): response is BoxPlotResponse {\n\treturn !isErrorResponse(response) && 'charts' in response && 'descrStats' in response\n}\n\n/** Type guard to check if response is a ViolinResponse */\nexport function isViolinResponse(response: ViolinBoxResponse): response is ViolinResponse {\n\treturn !isErrorResponse(response) && 'min' in response && 'max' in response\n}\n\n/** Violin response types */\ninterface BinsEntries {\n\tx0: number\n\tx1: number\n\tdensity: number\n}\n\ninterface ValuesEntries {\n\tid: string\n\tlabel: string\n\tvalue: number\n}\n\ninterface PValueEntries {\n\tvalue?: string\n\thtml?: string\n}\n\ntype ViolinDensity = {\n\tbins: BinsEntries[]\n\tdensityMax: number\n\tdensityMin: number\n}\n\nexport type ViolinPlotEntry = {\n\tcolor: string\n\tchartId: string\n\tdensity: ViolinDensity\n\tlabel: string\n\tplotValueCount: number\n\tseriesId: string\n\tsrc: string\n\tsummaryStats: ValuesEntries[]\n}\n\nexport type ViolinResponse = {\n\tbins: { [index: string]: any }\n\tcharts: {\n\t\t[index: string]: {\n\t\t\tchartId: string\n\t\t\tplots: ViolinPlotEntry[]\n\t\t\tpvalues?: PValueEntries[][]\n\t\t}\n\t}\n\tmin: number\n\tmax: number\n\tuncomputableValues: { [index: string]: number }[] | null\n\tdescrStats?: DescrStats\n}\n\n/** Boxplot response types */\nexport type BoxPlotData = {\n\tw1: number | undefined\n\tw2: number | undefined\n\tp05: number\n\tp25: number\n\tp50: number\n\tp75: number\n\tp95: number\n\tiqr: number\n\tout: { value: number }[]\n}\n\nexport type BoxPlotEntry = {\n\tboxplot: BoxPlotData & { label: string }\n\tcolor?: string\n\tdescrStats: DescrStats\n\tisHidden?: boolean\n\tkey: string\n\tseriesId?: string\n}\n\nexport type BoxPlotChartEntry = {\n\tchartId: string\n\tplots: BoxPlotEntry[]\n\tsampleCount: number\n\twilcoxon?: [{ value: string }, { value: string }, { html: string }][]\n}\n\nexport type BoxPlotResponse = {\n\tabsMin?: number\n\tabsMax?: number\n\tbins?: {\n\t\t[index: string]: any\n\t}\n\tcharts: {\n\t\t[chartId: string]: BoxPlotChartEntry\n\t}\n\tdescrStats: DescrStats\n\tuncomputableValues: { label: string; value: number }[] | null\n}\n\nexport const violinBoxPayload: RoutePayload = {\n\trequest: {\n\t\ttypeId: 'ViolinBoxRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'ViolinBoxResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'violin',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'aaclassic_5', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tdevicePixelRatio: 2,\n\t\t\t\t\tsvgw: 200,\n\t\t\t\t\torientation: 'horizontal',\n\t\t\t\t\tdatasymbol: 'rug',\n\t\t\t\t\tradius: 5,\n\t\t\t\t\tisLogScale: false\n\t\t\t\t}\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'box',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'agedx', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\toverlayTw: {\n\t\t\t\t\t\tterm: { id: 'sex', type: 'categorical' }\n\t\t\t\t\t},\n\t\t\t\t\torderByMedian: true\n\t\t\t\t}\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "import type { RoutePayload } from './routeApi.ts'\nimport type { WSIClass } from '../dataset.ts'\nimport type { Annotation, Prediction } from './aiProjectSelectedWSImages.ts'\n\nexport type SampleWSImagesRequest = {\n\tgenome: string\n\tdslabel: string\n\tsample_id: string\n\twsimage: string\n}\n\nexport type SampleWSImagesResponse = {\n\tsampleWSImages: WSImage[]\n}\n\nexport class WSImage {\n\tid?: number\n\tfilename: string\n\tmetadata?: string\n\tpredictionLayers?: Array<string>\n\tannotations?: Array<Annotation>\n\tpredictions?: Array<Prediction>\n\tclasses?: Array<WSIClass>\n\t/** ds defined uncertainity labels and colors */\n\tuncertainty?: any\n\t/** Color to highlight active patches */\n\tactivePatchColor?: string\n\t/** Tile size in pixels needed for AI scripts */\n\ttileSize?: number\n\n\tconstructor(filename: string) {\n\t\tthis.filename = filename\n\t}\n}\n\nexport const sampleWSImagesPayload: RoutePayload = {\n\trequest: {\n\t\ttypeId: 'SampleWSImagesRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'SampleWSImagesResponse'\n\t}\n\t// examples: []\n}\n"],
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+}