@sjcrh/proteinpaint-client 2.182.0 → 2.182.1

package/dist/chunk-DQGSCCI3.js

@@ -0,0 +1,100 @@
+import {
+  SearchHandler,
+  fillTermWrapper,
+  table2col,
+  termsettingInit
+} from "./chunk-NVB7MQLH.js";
+
+// plots/summarizeMutationDiagnosis.ts
+async function makeChartBtnMenu(holder, chartsInstance) {
+  let dictTw;
+  {
+    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
+    if (!t) throw "defaultTw4correlationPlot missing";
+    dictTw = structuredClone(t);
+    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+  }
+  const table = table2col({
+    holder: holder.append("div"),
+    margin: "0px 10px 10px 10px",
+    cellPadding: "10px"
+  });
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Mutation Variable");
+    const searchDiv = td2.append("div");
+    const geneSearchInst = new SearchHandler();
+    geneSearchInst.init({
+      holder: searchDiv,
+      app: chartsInstance.app,
+      // required to supply "opts.app.vocabApi" for the search ui
+      genomeObj: chartsInstance.app.opts.genome,
+      msg: "Hit ENTER to launch plot.",
+      callback: async (geneTw) => {
+        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
+        launchPlot({
+          tw1: dictTw,
+          tw2: geneTw,
+          chartsInstance,
+          holder
+        });
+      }
+    });
+    searchDiv.style("padding", "0px 0px 5px 0px");
+  }
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Compare Mutations Against");
+    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
+    const pill = await termsettingInit({
+      menuOptions: "{edit,replace}",
+      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
+      target="filter" works for gdc since in gdc ds it is overriding filter to dict
+      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
+      maybe this is okay for non-gdc ds as the default dictTw is meaningful
+      */
+      usecase: { target: "filter" },
+      vocabApi: chartsInstance.app.vocabApi,
+      holder: pillDiv,
+      callback: async (tw) => {
+        waitDiv.text("LOADING ...");
+        try {
+          await pill.main(tw);
+          dictTw = tw;
+          waitDiv.text("Click to edit/replace the variable before searching gene.");
+        } catch (e) {
+          waitDiv.text("Error: " + (e.message || e));
+        }
+      }
+    });
+    try {
+      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+      await pill.main(dictTw);
+      waitDiv.text("Click to edit/replace the variable before searching gene.");
+    } catch (e) {
+      waitDiv.text("Error: " + (e.message || e));
+    }
+  }
+}
+function launchPlot({ tw1, tw2, chartsInstance, holder }) {
+  const chart = {
+    config: {
+      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
+      // TODO define sandbox header with gene+term name
+      term: tw1,
+      term2: tw2
+    }
+  };
+  chartsInstance.plotCreate(chart);
+  holder.selectAll("*").remove();
+  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
+  setTimeout(() => {
+    holder.style("display", "none");
+  }, 1e3);
+}
+
+export {
+  makeChartBtnMenu,
+  launchPlot
+};
+//# sourceMappingURL=chunk-DQGSCCI3.js.map

package/dist/chunk-EWGMLVC7.js

@@ -0,0 +1,34 @@
+import {
+  appInit
+} from "./chunk-NVB7MQLH.js";
+import {
+  TermTypes
+} from "./chunk-6ITDJ5UR.js";
+
+// termdb/handlers/ssGSEA.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const genesetDbName = Object.keys(opts.genomeObj.termdbs || {})[0];
+    if (!genesetDbName) throw "genesetDbName missing";
+    await appInit({
+      holder: opts.holder,
+      state: {
+        dslabel: genesetDbName,
+        genome: opts.genomeObj.name,
+        nav: { header_mode: "search_only" }
+      },
+      tree: {
+        click_term: (term) => {
+          this.callback({ id: term.id, type: TermTypes.SSGSEA, name: term.name });
+        }
+      }
+    });
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-EWGMLVC7.js.map

package/dist/chunk-F7PB5HGT.js

@@ -0,0 +1,148 @@
+import {
+  storeInit
+} from "./chunk-ZTKQLABY.js";
+import {
+  recoverInit
+} from "./chunk-HZETQJGD.js";
+import {
+  AppBase,
+  sayerror,
+  vocabInit
+} from "./chunk-NVB7MQLH.js";
+import {
+  importPlot
+} from "./chunk-4JON7TLI.js";
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import {
+  AppApi
+} from "./chunk-MVTCBVSX.js";
+
+// plots/plot.app.ts
+var PlotApp = class _PlotApp extends AppBase {
+  constructor(opts, api) {
+    super(opts);
+    this.components = {};
+    this.wasDestroyed = false;
+    this.api = api;
+    this.type = _PlotApp.type;
+    this.dom = this.getDom(opts);
+  }
+  static {
+    this.type = "app";
+  }
+  getDom(opts) {
+    const dom = {
+      holder: opts.holder,
+      errdiv: opts.holder.append("div"),
+      plotDiv: opts.holder.append("div")
+    };
+    const controls = opts.violin?.mode == "minimal" ? null : opts.holder.append("div").style("white-space", "nowrap");
+    if (controls) {
+      dom.plotControls = controls.append("div").style("display", "inline-block");
+      dom.recoverControls = controls.append("div").style("display", "inline-block");
+    }
+    return dom;
+  }
+  async preApiFreeze(api) {
+    try {
+      api.tip = new Menu({ padding: "5px" });
+      api.printError = (e) => this.printError(e);
+      const vocab = this.opts.state.vocab;
+      api.vocabApi = this.opts.vocabApi ? this.opts.vocabApi : await vocabInit({
+        app: api,
+        state: {
+          vocab: {
+            // either (genome + dslabel) XOR (terms) can be undefined
+            genome: vocab?.genome || this.opts.state.genome,
+            dslabel: vocab?.dslabel || this.opts.state.dslabel,
+            terms: vocab?.terms
+          }
+        },
+        fetchOpts: this.opts.fetchOpts
+      });
+      this.opts.state.vocab = api.vocabApi.vocab;
+    } catch (e) {
+      console.log(`preApiFreeze error`, e);
+      throw e;
+    }
+  }
+  async init() {
+    try {
+      this.opts.state.nav = { header_mode: "hidden" };
+      this.store = await storeInit({ app: this.api, state: this.opts.state });
+      this.state = await this.store.copyState();
+      this.components = {
+        plots: {}
+      };
+      if (this.opts.app?.features?.includes("recover"))
+        this.components.recover = await recoverInit({
+          app: this.api,
+          holder: this.dom.recoverControls,
+          // TODO: ???? may limit the tracked state to only the filter, activeCohort ???
+          getState: (appState) => appState,
+          //reactsTo: action => true, //action.type != 'plot_edit' || action.type == 'app_refresh',
+          maxHistoryLen: 10
+        });
+      if (this.opts.app?.doNotAwaitInitRender) {
+        this.api.dispatch();
+      } else {
+        await this.api.dispatch();
+      }
+    } catch (e) {
+      this.printError(e);
+      throw e;
+    }
+  }
+  async main() {
+    this.api.vocabApi.main();
+    for (const id in this.components.plots) {
+      const plot = this.components.plots[id];
+      if (!this.state.plots.find((p) => p.id === plot.id)) {
+        plot.destroy();
+        delete this.components.plots[id];
+      }
+    }
+    for (const plot of this.state.plots.values()) {
+      if (plot.parentId) continue;
+      if (!this.components.plots[plot.id]) {
+        const holder = this.opts?.app?.getPlotHolder ? this.opts.app.getPlotHolder(plot, this.dom.holder) : this.dom.holder.append("div");
+        if (!this.dom.plotDiv) this.dom.plotDiv = holder;
+        const { componentInit } = await importPlot(plot.chartType);
+        const plotApi = await componentInit({
+          id: plot.id,
+          app: this.api,
+          holder,
+          controls: this.dom.plotControls
+        });
+        this.components.plots[plot.id] = plotApi;
+      }
+    }
+  }
+  printError(e) {
+    sayerror(this.dom.errdiv, "Error: " + (e.message || e));
+    if (e.stack) console.log(e.stack);
+    this.bus.emit("error");
+  }
+  skipPrevActionAbort(action) {
+    if (!action) return false;
+    if (action.type.startsWith("filter")) return false;
+    if (action.type.startsWith("cohort")) return false;
+    if (action.type == "app_refresh") {
+      if (action.subactions) {
+        return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
+      }
+    }
+    return true;
+  }
+  destroy() {
+    if (this.dom?.holder) this.dom.holder.selectAll("*").remove();
+  }
+};
+var appInit = AppApi.getInitFxn(PlotApp);
+
+export {
+  appInit
+};
+//# sourceMappingURL=chunk-F7PB5HGT.js.map

package/dist/chunk-FVWCYGJL.js

@@ -0,0 +1,121 @@
+import {
+  roundValueAuto
+} from "./chunk-L4QG7XZE.js";
+import {
+  brushX
+} from "./chunk-SEEYV6P2.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// filter/tvs.density.js
+function addBrushes(self, new_brush_location) {
+  const brushes = self.num_obj.brushes;
+  const maxvalue = self.num_obj.density_data.max;
+  const minvalue = self.num_obj.density_data.min;
+  const rawDecile = (maxvalue - minvalue) / 10;
+  const decile = self.tvs.term.type == "integer" ? Math.floor(rawDecile) : rawDecile;
+  for (const [i, r] of self.num_obj.ranges.entries()) {
+    const _b = brushes.find((b) => b.orig === r);
+    let brush;
+    if (!_b) {
+      brush = { orig: r, range: JSON.parse(JSON.stringify(r)) };
+      brushes.push(brush);
+    } else {
+      brush = _b;
+    }
+    if (r.start === "") {
+      if (new_brush_location == "center") brush.range.start = minvalue + decile * 4;
+      else brush.range.start = minvalue + decile * 8;
+    }
+    if (r.stop === "") {
+      if (new_brush_location == "center") brush.range.stop = minvalue + decile * 6;
+      else brush.range.stop = Math.floor(maxvalue);
+    }
+  }
+  const range_brushes = self.num_obj.brush_g.selectAll(".range_brush").data(brushes, (d) => brushes.indexOf(d));
+  range_brushes.exit().remove();
+  range_brushes.each(function(d, i) {
+    select_default(this).selectAll(".overlay").style("pointer-events", "all");
+  });
+  range_brushes.enter().append("g").attr("class", "range_brush").each(function(brush, i) {
+    applyBrush(self, this, brush, i);
+  });
+}
+function applyBrush(self, elem, brush) {
+  if (!brush.elem) brush.elem = select_default(elem);
+  const range = brush.range;
+  const plot_size = self.num_obj.plot_size;
+  const xscale = self.num_obj.xscale;
+  const maxvalue = self.num_obj.density_data.max;
+  const minvalue = self.num_obj.density_data.min;
+  brush.d3brush = brushX().extent([
+    [0, 0],
+    [plot_size.width, plot_size.height]
+  ]).on("brush", function(event, d) {
+    const s = event.selection;
+    if (!s) return;
+    const inputRange = brush.rangeInput.getRange();
+    if (inputRange?.value != void 0) {
+      brush.range = inputRange;
+      return;
+    }
+    updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, self.tvs.term.type);
+    const [start, stop] = setStartStopDisplays(range, inputRange);
+    brush.rangeInput.getInput().node().value = `${start} x ${stop}`;
+  }).on("end", function() {
+    brush.elem.selectAll(".overlay").style("pointer-events", "none");
+  });
+  const brush_start = range.startunbounded ? minvalue : range.start;
+  const brush_stop = range.stopunbounded ? maxvalue : range.stop;
+  brush.init = () => {
+    if (range.value == void 0)
+      brush.elem.call(brush.d3brush).call(brush.d3brush.move, [brush_start, brush_stop].map(xscale));
+  };
+  if (range.startunbounded) delete range.start;
+  if (range.stopunbounded) delete range.stop;
+  brush.elem.selectAll(".selection").style(
+    "fill",
+    brush.orig.start === "" && brush.orig.stop === "" || JSON.stringify(range) != JSON.stringify(brush.orig) ? "#23cba7" : "#777777"
+  );
+}
+function updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, type) {
+  range.start = convertRangeValue(xscale, s[0]);
+  range.stop = convertRangeValue(xscale, s[1]);
+  const min = roundValueAuto(Number(minvalue));
+  const max = roundValueAuto(Number(maxvalue));
+  if (range.start < min) range.start = min;
+  if (range.stop > max) range.stop = max;
+  range.startunbounded = min == range.start && inputRange.startunbounded;
+  range.stopunbounded = max == range.stop && inputRange.stopunbounded;
+  if (type == "integer") {
+    range.start = range.startunbounded ? "" : Math.round(range.start);
+    range.stop = range.stopunbounded ? "" : Math.round(range.stop);
+  }
+}
+function setStartStopDisplays(range, inputRange) {
+  const start = range.startunbounded ? "" : inputRange.startinclusive ? `${range.start} <=` : `${range.start} <`;
+  const stop = range.stopunbounded ? "" : inputRange.stopinclusive ? `<= ${range.stop}` : `< ${range.stop}`;
+  return [start, stop];
+}
+function convertRangeValue(xscale, sidx) {
+  const value = Number(xscale.invert(sidx));
+  return roundValueAuto(value);
+}
+function addNewBrush(self, new_brush_location = "end", callback) {
+  const new_range = { start: "", stop: "", index: self.tvs.ranges.length };
+  self.num_obj.ranges.push(new_range);
+  const brush = { orig: new_range, range: JSON.parse(JSON.stringify(new_range)) };
+  self.num_obj.brushes.push(brush);
+  addBrushes(self, new_brush_location);
+  if (callback) callback();
+  brush.init();
+}
+
+export {
+  addBrushes,
+  updateTempRanges,
+  setStartStopDisplays,
+  addNewBrush
+};
+//# sourceMappingURL=chunk-FVWCYGJL.js.map

package/dist/chunk-G7QKLA54.js

@@ -0,0 +1,92 @@
+import {
+  getPlotConfig
+} from "./chunk-YDWRIMCT.js";
+import {
+  fillTermWrapper
+} from "./chunk-NVB7MQLH.js";
+import {
+  copyMerge
+} from "./chunk-MVTCBVSX.js";
+import {
+  TermTypes,
+  numericTypes
+} from "./chunk-6ITDJ5UR.js";
+
+// plots/matrix/hierCluster.config.js
+async function getPlotConfig2(opts = {}, app) {
+  opts.chartType = "hierCluster";
+  const config = await getPlotConfig(opts, app);
+  delete config.genes;
+  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 hierClusterSubTypeOverrides = app.vocabApi.termdbConfig[`${config.dataType}Cluster`] || {};
+  copyMerge(
+    config.settings.hierCluster,
+    overrides.settings,
+    opts.settings?.hierCluster || {},
+    hierClusterSubTypeOverrides.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 == TermTypes.GENE_EXPRESSION || config.dataType == TermTypes.METABOLITE_INTENSITY || config.dataType == TermTypes.PROTEOME_ABUNDANCE) {
+          tw.term.type = config.dataType;
+        } else {
+          throw `term type missing and cannot be assigned by 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`;
+      }
+      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) {
+  return twType == grpType;
+}
+
+export {
+  getPlotConfig2 as getPlotConfig
+};
+//# sourceMappingURL=chunk-G7QKLA54.js.map

package/dist/chunk-HWHG63LH.js

@@ -0,0 +1,148 @@
+import {
+  NumericModes
+} from "./chunk-6ITDJ5UR.js";
+
+// plots/proteomeAbundance.js
+function renderAssayAndCohortRadios({
+  holder,
+  assays,
+  selectedProteomeDetails,
+  onChange,
+  assayTitle = "Assay Type",
+  cohortTitle = "Cohort"
+}) {
+  const assayEntries = Object.entries(assays || {});
+  if (!assayEntries.length) {
+    holder.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No proteome assays available.");
+    return {
+      getSelected: () => ({ assay: void 0, cohort: void 0 })
+    };
+  }
+  const initialProteomeDetails = selectedProteomeDetails || {};
+  const assayRadioName = `sjpp-proteome-assay-${Math.random().toString().slice(-6)}`;
+  const cohortRadioName = `sjpp-proteome-cohort-${Math.random().toString().slice(-6)}`;
+  let selectedAssay = assays[initialProteomeDetails.assay] ? initialProteomeDetails.assay : assayEntries[0][0];
+  let selectedCohort = initialProteomeDetails.cohort;
+  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(assayTitle);
+  const assayListDiv = holder.append("div").style("margin-bottom", "10px");
+  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(cohortTitle);
+  const cohortListDiv = holder.append("div");
+  for (const [assayKey] of assayEntries) {
+    const assayLabel = assayListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
+    assayLabel.append("input").attr("type", "radio").attr("name", assayRadioName).attr("value", assayKey).property("checked", assayKey === selectedAssay).style("margin-right", "6px").on("change", () => {
+      selectedAssay = assayKey;
+      selectedCohort = void 0;
+      renderCohortOptions();
+      onChange?.({ assay: selectedAssay, cohort: selectedCohort });
+    });
+    assayLabel.append("span").text(assayKey);
+  }
+  renderCohortOptions();
+  onChange?.({ assay: selectedAssay, cohort: selectedCohort });
+  return {
+    getSelected: () => ({ assay: selectedAssay, cohort: selectedCohort })
+  };
+  function renderCohortOptions() {
+    cohortListDiv.selectAll("*").remove();
+    const cohorts = Object.keys(assays[selectedAssay]?.cohorts || {});
+    if (!cohorts.length) {
+      selectedCohort = void 0;
+      cohortListDiv.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No cohorts available.");
+      return;
+    }
+    if (!selectedCohort || !assays[selectedAssay]?.cohorts?.[selectedCohort]) {
+      selectedCohort = cohorts.includes(initialProteomeDetails.cohort) ? initialProteomeDetails.cohort : cohorts[0];
+    }
+    for (const cohortKey of cohorts) {
+      const cohortLabel = cohortListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
+      cohortLabel.append("input").attr("type", "radio").attr("name", cohortRadioName).attr("value", cohortKey).property("checked", cohortKey === selectedCohort).style("margin-right", "6px").on("change", () => {
+        selectedCohort = cohortKey;
+        onChange?.({ assay: selectedAssay, cohort: selectedCohort });
+      });
+      cohortLabel.append("span").text(cohortKey);
+    }
+  }
+}
+function makeChartBtnMenu(holder, chartsInstance) {
+  chartsInstance.dom.tip.clear();
+  const assays = chartsInstance.state.termdbConfig?.queries?.proteome?.assays || {};
+  const menuDiv = holder.append("div");
+  let selectedProteomeDetails;
+  let launchOption;
+  const syncLaunchButtonState = () => {
+    if (!launchOption) return;
+    if (selectedProteomeDetails?.cohort) launchOption.style("opacity", 1).style("pointer-events", "auto");
+    else launchOption.style("opacity", 0.5).style("pointer-events", "none");
+  };
+  renderAssayAndCohortRadios({
+    holder: menuDiv,
+    assays,
+    onChange: (proteomeDetails) => {
+      selectedProteomeDetails = proteomeDetails;
+      syncLaunchButtonState();
+    }
+  });
+  launchOption = menuDiv.append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn sja_sharp_border").style("display", "block").style("margin", "10px auto 10px").text("Select Protein").on("click", () => {
+    if (!selectedProteomeDetails?.cohort) return;
+    const { assay, cohort } = selectedProteomeDetails;
+    const assayCohortTitle = `${assay}: ${cohort}`;
+    const chart = {
+      label: "Protein Abundance",
+      chartType: "proteomeAbundance",
+      usecase: {
+        target: "proteomeAbundance",
+        detail: "term",
+        proteomeDetails: { assay, cohort },
+        label: `Assay: ${assay}; Cohort: ${cohort}`
+      },
+      processSelection: (termlst) => termlst,
+      updateActionBySelectedTerms: (action, termlst) => {
+        action.config.assayCohortTitle = assayCohortTitle;
+        const { assay: assay2, cohort: cohort2 } = selectedProteomeDetails;
+        action.config.proteomeDetails = { assay: assay2, cohort: cohort2 };
+        const cohortSelected = chartsInstance.state.termdbConfig.queries.proteome.assays[assay2].cohorts[cohort2];
+        if (cohortSelected.filter) action.config.filter = toTvslstFilter(cohortSelected.filter);
+        const twlst = termlst.map((term) => {
+          const t = structuredClone(term);
+          t.proteomeDetails = { assay: assay2, cohort: cohort2 };
+          return { term: t, q: { mode: NumericModes.continuous } };
+        });
+        if (twlst.length == 1) {
+          action.config.chartType = "summary";
+          action.config.term = twlst[0];
+          if (cohortSelected.overlayTerm)
+            action.config.term2 = { term: structuredClone(cohortSelected.overlayTerm), q: {} };
+          return;
+        }
+        if (twlst.length == 2) {
+          action.config.chartType = "summary";
+          action.config.term = twlst[0];
+          action.config.term2 = twlst[1];
+          return;
+        }
+        action.config.chartType = "hierCluster";
+        action.config.dataType = "proteomeAbundance";
+        action.config.termgroups = [{ name: "Protein Abundance Cluster", lst: twlst, type: "hierCluster" }];
+      }
+    };
+    chartsInstance.dom.tip.clear();
+    chartsInstance.showTree_selectlst(chart);
+  });
+  syncLaunchButtonState();
+}
+function toTvslstFilter(filterConfig) {
+  if (filterConfig && Array.isArray(filterConfig) && filterConfig.length)
+    return {
+      type: "tvslst",
+      in: true,
+      join: filterConfig.length > 1 ? "and" : "",
+      lst: filterConfig.map((tvs) => ({ type: "tvs", tvs }))
+    };
+}
+
+export {
+  renderAssayAndCohortRadios,
+  makeChartBtnMenu,
+  toTvslstFilter
+};
+//# sourceMappingURL=chunk-HWHG63LH.js.map

package/dist/chunk-HWHG63LH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/proteomeAbundance.js"],
+  "sourcesContent": ["import { NumericModes } from '#shared/terms.js'\n\nexport function renderAssayAndCohortRadios({\n\tholder,\n\tassays,\n\tselectedProteomeDetails,\n\tonChange,\n\tassayTitle = 'Assay Type',\n\tcohortTitle = 'Cohort'\n}) {\n\tconst assayEntries = Object.entries(assays || {})\n\tif (!assayEntries.length) {\n\t\tholder.append('div').attr('class', 'sja_sharp_border').style('padding', '8px').text('No proteome assays available.')\n\t\treturn {\n\t\t\tgetSelected: () => ({ assay: undefined, cohort: undefined })\n\t\t}\n\t}\n\n\tconst initialProteomeDetails = selectedProteomeDetails || {}\n\n\tconst assayRadioName = `sjpp-proteome-assay-${Math.random().toString().slice(-6)}`\n\tconst cohortRadioName = `sjpp-proteome-cohort-${Math.random().toString().slice(-6)}`\n\n\tlet selectedAssay = assays[initialProteomeDetails.assay] ? initialProteomeDetails.assay : assayEntries[0][0]\n\tlet selectedCohort = initialProteomeDetails.cohort\n\n\tholder.append('div').style('margin', '3px 5px').style('padding', '3px 5px').style('font-weight', 600).text(assayTitle)\n\tconst assayListDiv = holder.append('div').style('margin-bottom', '10px')\n\n\tholder\n\t\t.append('div')\n\t\t.style('margin', '3px 5px')\n\t\t.style('padding', '3px 5px')\n\t\t.style('font-weight', 600)\n\t\t.text(cohortTitle)\n\tconst cohortListDiv = holder.append('div')\n\n\tfor (const [assayKey] of assayEntries) {\n\t\tconst assayLabel = assayListDiv\n\t\t\t.append('label')\n\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t.style('display', 'block')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.style('padding', '6px 8px')\n\t\t\t.style('border-radius', '4px')\n\n\t\tassayLabel\n\t\t\t.append('input')\n\t\t\t.attr('type', 'radio')\n\t\t\t.attr('name', assayRadioName)\n\t\t\t.attr('value', assayKey)\n\t\t\t.property('checked', assayKey === selectedAssay)\n\t\t\t.style('margin-right', '6px')\n\t\t\t.on('change', () => {\n\t\t\t\tselectedAssay = assayKey\n\t\t\t\tselectedCohort = undefined\n\t\t\t\trenderCohortOptions()\n\t\t\t\tonChange?.({ assay: selectedAssay, cohort: selectedCohort })\n\t\t\t})\n\t\tassayLabel.append('span').text(assayKey)\n\t}\n\n\trenderCohortOptions()\n\tonChange?.({ assay: selectedAssay, cohort: selectedCohort })\n\n\treturn {\n\t\tgetSelected: () => ({ assay: selectedAssay, cohort: selectedCohort })\n\t}\n\n\tfunction renderCohortOptions() {\n\t\tcohortListDiv.selectAll('*').remove()\n\t\tconst cohorts = Object.keys(assays[selectedAssay]?.cohorts || {})\n\t\tif (!cohorts.length) {\n\t\t\tselectedCohort = undefined\n\t\t\tcohortListDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '8px')\n\t\t\t\t.text('No cohorts available.')\n\t\t\treturn\n\t\t}\n\n\t\tif (!selectedCohort || !assays[selectedAssay]?.cohorts?.[selectedCohort]) {\n\t\t\tselectedCohort = cohorts.includes(initialProteomeDetails.cohort) ? initialProteomeDetails.cohort : cohorts[0]\n\t\t}\n\n\t\tfor (const cohortKey of cohorts) {\n\t\t\tconst cohortLabel = cohortListDiv\n\t\t\t\t.append('label')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('padding', '6px 8px')\n\t\t\t\t.style('border-radius', '4px')\n\t\t\tcohortLabel\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'radio')\n\t\t\t\t.attr('name', cohortRadioName)\n\t\t\t\t.attr('value', cohortKey)\n\t\t\t\t.property('checked', cohortKey === selectedCohort)\n\t\t\t\t.style('margin-right', '6px')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tselectedCohort = cohortKey\n\t\t\t\t\tonChange?.({ assay: selectedAssay, cohort: selectedCohort })\n\t\t\t\t})\n\n\t\t\tcohortLabel.append('span').text(cohortKey)\n\t\t}\n\t}\n}\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\tchartsInstance.dom.tip.clear()\n\tconst assays = chartsInstance.state.termdbConfig?.queries?.proteome?.assays || {}\n\tconst menuDiv = holder.append('div')\n\n\tlet selectedProteomeDetails\n\tlet launchOption\n\n\tconst syncLaunchButtonState = () => {\n\t\tif (!launchOption) return\n\t\tif (selectedProteomeDetails?.cohort) launchOption.style('opacity', 1).style('pointer-events', 'auto')\n\t\telse launchOption.style('opacity', 0.5).style('pointer-events', 'none')\n\t}\n\n\trenderAssayAndCohortRadios({\n\t\tholder: menuDiv,\n\t\tassays,\n\t\tonChange: proteomeDetails => {\n\t\t\tselectedProteomeDetails = proteomeDetails\n\t\t\tsyncLaunchButtonState()\n\t\t}\n\t})\n\n\tlaunchOption = menuDiv\n\t\t.append('button')\n\t\t.attr('class', 'sjpp_apply_btn sja_filter_tag_btn sja_sharp_border')\n\t\t.style('display', 'block')\n\t\t.style('margin', '10px auto 10px')\n\t\t.text('Select Protein')\n\t\t.on('click', () => {\n\t\t\tif (!selectedProteomeDetails?.cohort) return\n\t\t\tconst { assay, cohort } = selectedProteomeDetails\n\t\t\tconst assayCohortTitle = `${assay}: ${cohort}`\n\t\t\tconst chart = {\n\t\t\t\tlabel: 'Protein Abundance',\n\t\t\t\tchartType: 'proteomeAbundance',\n\t\t\t\tusecase: {\n\t\t\t\t\ttarget: 'proteomeAbundance',\n\t\t\t\t\tdetail: 'term',\n\t\t\t\t\tproteomeDetails: { assay, cohort },\n\t\t\t\t\tlabel: `Assay: ${assay}; Cohort: ${cohort}`\n\t\t\t\t},\n\t\t\t\tprocessSelection: termlst => termlst,\n\t\t\t\tupdateActionBySelectedTerms: (action, termlst) => {\n\t\t\t\t\taction.config.assayCohortTitle = assayCohortTitle\n\t\t\t\t\tconst { assay, cohort } = selectedProteomeDetails\n\t\t\t\t\taction.config.proteomeDetails = { assay, cohort }\n\t\t\t\t\tconst cohortSelected = chartsInstance.state.termdbConfig.queries.proteome.assays[assay].cohorts[cohort]\n\t\t\t\t\tif (cohortSelected.filter) action.config.filter = toTvslstFilter(cohortSelected.filter)\n\t\t\t\t\tconst twlst = termlst.map(term => {\n\t\t\t\t\t\tconst t = structuredClone(term)\n\t\t\t\t\t\tt.proteomeDetails = { assay, cohort }\n\t\t\t\t\t\treturn { term: t, q: { mode: NumericModes.continuous } }\n\t\t\t\t\t})\n\n\t\t\t\t\tif (twlst.length == 1) {\n\t\t\t\t\t\taction.config.chartType = 'summary'\n\t\t\t\t\t\taction.config.term = twlst[0]\n\t\t\t\t\t\tif (cohortSelected.overlayTerm)\n\t\t\t\t\t\t\taction.config.term2 = { term: structuredClone(cohortSelected.overlayTerm), q: {} }\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tif (twlst.length == 2) {\n\t\t\t\t\t\taction.config.chartType = 'summary'\n\t\t\t\t\t\taction.config.term = twlst[0]\n\t\t\t\t\t\taction.config.term2 = twlst[1]\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\n\t\t\t\t\taction.config.chartType = 'hierCluster'\n\t\t\t\t\taction.config.dataType = 'proteomeAbundance'\n\t\t\t\t\taction.config.termgroups = [{ name: 'Protein Abundance Cluster', lst: twlst, type: 'hierCluster' }]\n\t\t\t\t}\n\t\t\t}\n\t\t\tchartsInstance.dom.tip.clear()\n\t\t\tchartsInstance.showTree_selectlst(chart)\n\t\t})\n\n\tsyncLaunchButtonState()\n}\n\nexport function toTvslstFilter(filterConfig) {\n\tif (filterConfig && Array.isArray(filterConfig) && filterConfig.length)\n\t\treturn {\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: filterConfig.length > 1 ? 'and' : '',\n\t\t\tlst: filterConfig.map(tvs => ({ type: 'tvs', tvs }))\n\t\t}\n}\n"],
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+  "names": ["assay", "cohort"]
+}