@sjcrh/proteinpaint-client 2.206.0 → 2.207.0

package/dist/brainImaging-SPRC3QFB.js

@@ -1,515 +0,0 @@
-import {
-  PlotBase,
-  controlsInit,
-  fetchBrainImagingSamples,
-  fillTermWrapper,
-  getCombinedTermFilter,
-  getT0T2defaultQ,
-  renderTable,
-  sayerror,
-  svgLegend
-} from "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import {
-  require_debounce
-} from "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/brainImaging.ts
-var import_debounce = __toESM(require_debounce(), 1);
-var BrainImaging = class _BrainImaging extends PlotBase {
-  static {
-    this.type = "brainImaging";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _BrainImaging.type;
-    this.components = { controls: {} };
-    setInteractivity(this);
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const holder = this.opts.holder;
-    if (this.opts.header) {
-      const fileNames = state.config.selectedSampleFileNames;
-      const samplesLabel = fileNames.length < 3 ? fileNames.map((f) => f.split(".nii")[0]).join(", ") : `${fileNames.length} samples`;
-      this.opts.header.style("padding-left", "7px").style("color", "rgb(85, 85, 85)").html(`Brain Imaging: ${state.config.queryKey}/${samplesLabel}`);
-    }
-    const controlsHolder = holder.append("div").style("display", "inline-block").style("vertical-align", "top");
-    const rightDiv = holder.append("div").style("display", "inline-block").style("vertical-align", "top");
-    const headerHolder = rightDiv.append("div").style("display", "inline-block").style("vertical-align", "top").style("padding", "10px");
-    const contentHolder = rightDiv.append("div").style("vertical-align", "top");
-    const table = contentHolder.append("table").style("border-collapse", "collapse");
-    const headerTr = table.append("tr");
-    const contentTr = table.append("tr").style("background-color", "black");
-    const tdL = contentTr.append("td");
-    const tdF = contentTr.append("td");
-    const tdT = contentTr.append("td");
-    const legendHolder = contentHolder.append("svg").style("width", "100%").on("mouseup", this.legendLabelMouseup);
-    const legendMenu = new Menu({ padding: "0px" });
-    this.dom = {
-      headerHolder,
-      contentHolder,
-      headerTr,
-      tdL,
-      tdF,
-      tdT,
-      legendHolder,
-      legendMenu
-    };
-    this.addSliders(state);
-    const configInputsOptions = this.getConfigInputsOptions(state);
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: controlsHolder,
-        inputs: configInputsOptions
-      })
-    };
-    this.components.controls.on("downloadClick.brainImaging", () => {
-      const urls = [];
-      for (const key in this.imagesData)
-        for (const category in this.imagesData[key].dataUrls) {
-          const dataUrl = this.imagesData[key].dataUrls[category].url;
-          urls.push(dataUrl);
-        }
-      this.downloadImage(urls);
-    });
-    this.legendRenderer = svgLegend({ holder: this.dom.legendHolder });
-  }
-  addSliders(state) {
-    const settings = state.config.settings.brainImaging;
-    const dims = state.RefNIdata?.dimensions;
-    const maxL = (dims?.l || 193) - 1;
-    const maxF = (dims?.f || 229) - 1;
-    const maxT = (dims?.t || 193) - 1;
-    const tr = this.dom.headerTr;
-    let td = tr.append("td");
-    td.append("label").attr("for", "saggital").text("Sagittal:");
-    this.dom.saggitalSlider = td.append("input").attr("id", "saggital").attr("type", "range").attr("min", 0).attr("max", maxL).attr("value", settings.brainImageL).on("change", (e) => {
-      this.editBrainImage("brainImageL", e.target.value);
-    });
-    this.dom.saggitalInput = td.append("input").attr("type", "number").attr("min", 0).attr("max", maxL).attr("value", settings.brainImageL).on("change", (e) => {
-      this.editBrainImage("brainImageL", e.target.value);
-    }).style("vertical-align", "top");
-    td = tr.append("td");
-    td.append("label").attr("for", "coronal").text("Coronal:");
-    this.dom.coronalSlider = td.append("input").attr("type", "range").attr("min", 0).attr("max", maxF).attr("value", settings.brainImageF).on("change", (e) => {
-      this.editBrainImage("brainImageF", e.target.value);
-    });
-    this.dom.coronalInput = td.append("input").attr("type", "number").attr("min", 0).attr("max", maxF).attr("value", settings.brainImageF).on("change", (e) => {
-      this.editBrainImage("brainImageF", e.target.value);
-    }).style("vertical-align", "top");
-    td = tr.append("td");
-    td.append("label").attr("for", "axial").text("Axial:");
-    this.dom.axialSlider = td.append("input").attr("id", "axial").attr("type", "range").attr("min", 0).attr("max", maxT).attr("value", settings.brainImageT).on("change", (e) => {
-      this.editBrainImage("brainImageT", e.target.value);
-    });
-    this.dom.axialInput = td.append("input").attr("type", "number").attr("min", 0).attr("max", maxT).attr("value", settings.brainImageT).on("change", (e) => {
-      this.editBrainImage("brainImageT", e.target.value);
-    });
-  }
-  editBrainImage(key, value) {
-    if (!value) return;
-    const settings = { [key]: Number(value) };
-    this.app.dispatch({ type: "plot_edit", id: this.id, config: { settings: { brainImaging: settings } } });
-  }
-  downloadImage(dataUrls) {
-    for (const dataUrl of dataUrls) {
-      const downloadImgName = "brainImaging";
-      const a = document.createElement("a");
-      document.body.appendChild(a);
-      a.addEventListener(
-        "click",
-        () => {
-          a.download = downloadImgName + ".png";
-          a.href = dataUrl;
-          document.body.removeChild(a);
-        },
-        false
-      );
-      a.click();
-    }
-  }
-  getConfigInputsOptions(state) {
-    if (state.config.selectedSampleFileNames.length == 1) return [];
-    const mandatoryConfigInputOptions = [
-      {
-        label: "Divide by",
-        type: "term",
-        chartType: "brainImaging",
-        configKey: "divideByTW",
-        title: "Categories to divide by",
-        usecase: { target: "brainImaging", detail: "term0" },
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: ["discrete"],
-        defaultQ4fillTW: getT0T2defaultQ()
-      },
-      {
-        label: "Color by",
-        type: "term",
-        chartType: "brainImaging",
-        configKey: "overlayTW",
-        title: "Categories to color the samples",
-        usecase: { target: "brainImaging", detail: "term2" },
-        vocabApi: this.app.vocabApi,
-        numericEditMenuVersion: ["discrete"],
-        defaultQ4fillTW: getT0T2defaultQ()
-      }
-    ];
-    return mandatoryConfigInputOptions;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    const termfilter = getCombinedTermFilter(appState, config.filter);
-    return {
-      config,
-      termfilter,
-      dslabel: appState.vocab.dslabel,
-      genome: appState.vocab.genome,
-      RefNIdata: appState.termdbConfig.queries.NIdata[config.queryKey]
-    };
-  }
-  async main() {
-    this.config = structuredClone(this.state.config);
-    this.settings = this.state.config.settings.brainImaging;
-    this.dom.saggitalSlider.property("value", this.settings.brainImageL);
-    this.dom.saggitalInput.property("value", this.settings.brainImageL);
-    this.dom.coronalSlider.property("value", this.settings.brainImageF);
-    this.dom.coronalInput.property("value", this.settings.brainImageF);
-    this.dom.axialSlider.property("value", this.settings.brainImageT);
-    this.dom.axialInput.property("value", this.settings.brainImageT);
-    let data;
-    try {
-      data = await Promise.all([
-        this.requestImage("l", this.settings.brainImageL),
-        this.requestImage("f", this.settings.brainImageF),
-        this.requestImage("t", this.settings.brainImageT)
-      ]);
-    } catch (e) {
-      this.showNoImage(e?.message || e);
-      return;
-    }
-    const failedIdx = data.findIndex((d) => !d || typeof d == "string" || d.error || !d.brainImage);
-    if (failedIdx != -1) {
-      const failed = data[failedIdx];
-      this.showNoImage(typeof failed == "string" && failed || failed?.error || "no brain imaging data");
-      return;
-    }
-    this.imagesData = {
-      brainImageL: { dataUrls: {}, td: this.dom.tdL, data: data[0] },
-      brainImageF: { dataUrls: {}, td: this.dom.tdF, data: data[1] },
-      brainImageT: { dataUrls: {}, td: this.dom.tdT, data: data[2] }
-    };
-    for (const img of Object.values(this.imagesData)) this.renderImages(img);
-    this.renderLegend();
-  }
-  // shown when image data could not be generated, e.g. the sample has no imaging file
-  showNoImage(message) {
-    for (const td of [this.dom.tdL, this.dom.tdF, this.dom.tdT]) td.selectAll("*").remove();
-    this.dom.tdL.append("div").style("color", "white").style("padding", "20px").style("white-space", "nowrap").text(String(message));
-    this.dom.legendHolder.selectAll("*").remove();
-  }
-  async requestImage(key, value) {
-    const body = {
-      genome: this.state.genome,
-      dslabel: this.state.dslabel,
-      refKey: this.state.config.queryKey,
-      [key]: value,
-      selectedSampleFileNames: this.state.config.selectedSampleFileNames,
-      divideByTW: this.state.config.divideByTW,
-      overlayTW: this.state.config.overlayTW,
-      legendFilter: this.state.config.legendFilter,
-      filter: this.state.termfilter?.filter
-    };
-    return await dofetch3("brainImaging", { body });
-  }
-  renderImages({ data, td, dataUrls }) {
-    this.legendValues = data.legend;
-    if (data.error) throw data.error;
-    for (const [termV, result] of Object.entries(data.brainImage)) {
-      dataUrls[termV] = result;
-    }
-    td.selectAll("*").remove();
-    for (const [termV, result] of Object.entries(dataUrls)) {
-      const imgResult = result;
-      if (this.state.config.divideByTW)
-        td.append("div").attr("class", "pp-chart-title").style("text-align", "center").text(`${termV} (n=${imgResult.catNum})`).style("font-weight", "600").style("color", "white").style("font-size", "24px").style("margin-bottom", "5px").style("margin-top", "5px").style("display", "block");
-      td.append("div").append("img").attr("src", imgResult.url);
-    }
-  }
-  renderLegend() {
-    const legendItems = [];
-    for (const [label, v] of Object.entries(this.legendValues)) {
-      const scale = linear([0, v.maxLength], [rgb("white").formatHex(), v.color]).clamp(true);
-      legendItems.push({
-        text: label == "default" ? "Combined Intensity" : label,
-        width: 140,
-        scale,
-        colors: ["white", v.color],
-        domain: [0, v.maxLength],
-        key: label,
-        crossedOut: v.crossedOut
-      });
-    }
-    this.legendItems = legendItems;
-    const legendRendererData = [
-      {
-        items: legendItems
-      }
-    ];
-    this.legendRenderer(legendRendererData, {
-      settings: {
-        fontsize: 16,
-        iconh: 14,
-        iconw: 14,
-        dimensions: {
-          xOffset: 0
-        }
-      }
-    });
-  }
-};
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.dom.tip.clear();
-  const menuDiv = holder.append("div");
-  if (chartsInstance.state.termdbConfig.queries.NIdata) {
-    const refDivs = [];
-    for (const refKey of Object.keys(chartsInstance.state.termdbConfig.queries.NIdata)) {
-      const refDiv = menuDiv.append("div");
-      refDivs.push(refDiv);
-      const refOption = refDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text(refKey).on("click", async () => {
-        for (const d of refDivs) if (d !== refDiv) d.style("display", "none");
-        refOption.attr("class", "").style("font-weight", "bold").style("padding", "5px");
-        refOption.on("click", null);
-        const body = {
-          genome: chartsInstance.opts.vocab.genome,
-          dslabel: chartsInstance.opts.vocab.dslabel,
-          refKey,
-          // restrict the sample table by the current cohort filter, if one is set
-          filter: chartsInstance.state.filter
-        };
-        let samples;
-        try {
-          const result = await fetchBrainImagingSamples(body);
-          samples = result.samples || [];
-        } catch (e) {
-          sayerror(refDiv, e?.message || String(e));
-          return;
-        }
-        const columns = await getTableColumns(chartsInstance, refKey);
-        let shownSamples = samples;
-        const selectedSamples = /* @__PURE__ */ new Set();
-        const updateSelections = (idxlst) => {
-          const checked = new Set(idxlst.map((i) => shownSamples[i]?.sample));
-          for (const s of shownSamples) {
-            if (!s.sample) continue;
-            if (checked.has(s.sample)) selectedSamples.add(s.sample);
-            else selectedSamples.delete(s.sample);
-          }
-        };
-        const debouncedRenderRows = (0, import_debounce.debounce)(() => renderRows(), 200);
-        const searchDiv = refDiv.append("div").style("padding", "5px 0px");
-        const searchInput = searchDiv.append("input").attr("type", "search").attr("placeholder", "Search samples").style("width", "200px").on("input", debouncedRenderRows);
-        const countLabel = searchDiv.append("span").style("margin-left", "10px").style("opacity", 0.6);
-        const tableDiv = refDiv.append("div");
-        const applybt = {
-          text: "Apply",
-          // unstyled button, found by testid since it carries no distinguishing class
-          dataTestId: "sjpp-brainImaging-apply",
-          /* fires on every checkbox change: keeps selectedSamples current, and
-          overrides the table's own disabling (which only considers visible rows)
-          so Apply stays usable when checked samples are hidden by the search */
-          onChange: (idxlst, button) => {
-            updateSelections(idxlst);
-            if (button) button.disabled = !selectedSamples.size;
-          },
-          callback: (indexes) => {
-            updateSelections(indexes);
-            if (!selectedSamples.size) return;
-            chartsInstance.dom.tip.hide();
-            const selectedSampleFileNames = [...selectedSamples].map((s) => s + ".nii");
-            chartsInstance.app.dispatch({
-              type: "plot_create",
-              config: {
-                chartType: "brainImaging",
-                queryKey: refKey,
-                selectedSampleFileNames
-              }
-            });
-          }
-        };
-        const renderRows = () => {
-          const str = searchInput.property("value").trim().toLowerCase();
-          shownSamples = !str ? samples : samples.filter((s) => Object.values(s).some((v) => v != void 0 && String(v).toLowerCase().includes(str)));
-          countLabel.text(
-            (str ? `${shownSamples.length} of ${samples.length} samples` : `${samples.length} samples`) + (selectedSamples.size ? `; ${selectedSamples.size} selected` : "")
-          );
-          const rows = getTableRows(shownSamples, chartsInstance.state, refKey);
-          tableDiv.selectAll("*").remove();
-          renderTable({
-            rows,
-            columns,
-            resize: true,
-            singleMode: false,
-            div: tableDiv,
-            maxHeight: "40vh",
-            header: { allowSort: true },
-            selectedRows: shownSamples.map((s, i) => selectedSamples.has(s.sample) ? i : -1).filter((i) => i >= 0),
-            buttons: [applybt],
-            buttonsToLeft: true
-          });
-        };
-        renderRows();
-      });
-    }
-  }
-}
-var brainImaging = getCompInit(BrainImaging);
-var componentInit = brainImaging;
-async function getPlotConfig(opts, app) {
-  const ref = app.vocabApi?.termdbConfig?.queries?.NIdata?.[opts.queryKey];
-  const parameters = ref?.parameters;
-  const dims = ref?.dimensions;
-  const settings = {
-    brainImaging: {
-      brainImageL: parameters?.l ?? (dims ? Math.floor(dims.l / 2) : 98),
-      brainImageF: parameters?.f ?? (dims ? Math.floor(dims.f / 2) : 81),
-      brainImageT: parameters?.t ?? (dims ? Math.floor(dims.t / 2) : 53)
-    }
-  };
-  const config = { chartType: "brainImaging", settings };
-  copyMerge(config, opts);
-  if (config.overlayTW) config.overlayTW = await fillTermWrapper(config.overlayTW, app.vocabApi);
-  if (config.divideByTW) config.divideByTW = await fillTermWrapper(config.divideByTW, app.vocabApi);
-  return config;
-}
-function getTableRows(samples, state, refKey) {
-  const rows = [];
-  for (const sample of samples) {
-    const row = [{ value: sample.sample }];
-    for (const c of state.termdbConfig.queries.NIdata[refKey].sampleColumns || []) {
-      row.push({ value: sample[c.termid] });
-    }
-    rows.push(row);
-  }
-  return rows;
-}
-async function getTableColumns(self, refKey) {
-  const columns = [{ label: "Sample", sortable: true }];
-  for (const c of self.state.termdbConfig.queries.NIdata[refKey].sampleColumns || []) {
-    columns.push({
-      label: (await self.app.vocabApi.getterm(c.termid)).name,
-      sortable: true
-    });
-  }
-  return columns;
-}
-function setInteractivity(self) {
-  self.legendLabelMouseup = (event) => {
-    const targetData = event.target.__data__;
-    if (!targetData || targetData.key == "default") return;
-    const legendMenu = self.dom.legendMenu.clear();
-    const legendMenuDiv = legendMenu.d.append("div");
-    const legendFilter = self.state.config.legendFilter ? [...self.state.config.legendFilter] : [];
-    const legendFilterIndex = legendFilter.indexOf(targetData.key);
-    if (legendFilterIndex !== -1 || legendFilter.length + 1 !== self.legendItems.length) {
-      legendMenuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text(legendFilterIndex == -1 ? "Hide" : "Show").on("click", () => {
-        legendMenu.hide();
-        if (legendFilterIndex == -1) legendFilter.push(targetData.key);
-        else legendFilter.splice(legendFilterIndex, 1);
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: { legendFilter }
-        });
-      });
-    }
-    legendMenuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show only").on("click", () => {
-      legendMenu.hide();
-      const legendFilter2 = [];
-      for (const legendCat of self.legendItems) {
-        if (legendCat.key !== targetData.key) legendFilter2.push(legendCat.key);
-      }
-      self.app.dispatch({
-        type: "plot_edit",
-        id: self.id,
-        config: { legendFilter: legendFilter2 }
-      });
-    });
-    legendMenuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show all").on("click", () => {
-      legendMenu.hide();
-      self.app.dispatch({
-        type: "plot_edit",
-        id: self.id,
-        config: { legendFilter: [] }
-      });
-    });
-    if (self.state.config.overlayTW.term.type != "geneVariant") {
-      let color = self.state.config.overlayTW?.term?.values?.[targetData.key]?.color || "red";
-      color = rgb(color).formatHex();
-      legendMenuDiv.append("div").attr("class", "sja_sharp_border").style("padding", "0px 10px").text("Color:").append("input").attr("type", "color").attr("value", color).on("change", (e) => {
-        self.changeColor(targetData.key, e.target.value);
-      });
-    }
-    legendMenu.showunder(event.target);
-  };
-  self.changeColor = async function(key, color) {
-    const tw = self.config.overlayTW;
-    if (!(tw.term.type == "geneVariant" && tw.q.type == "values") && tw.term.values[key])
-      tw.term.values[key].color = color;
-    else {
-      if (!tw.term.values) tw.term.values = {};
-      if (!tw.term.values[key]) tw.term.values[key] = {};
-      tw.term.values[key].color = color;
-    }
-    await self.app.dispatch({
-      type: "plot_edit",
-      id: self.id,
-      config: { overlayTW: tw }
-    });
-  };
-}
-export {
-  brainImaging,
-  componentInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=brainImaging-SPRC3QFB.js.map

package/dist/brainImaging-SPRC3QFB.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/brainImaging.ts"],
-  "sourcesContent": ["import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.ts'\nimport { controlsInit } from './controls'\nimport { getT0T2defaultQ } from './summaryQ.ts'\nimport { fillTermWrapper } from '#termsetting'\nimport { dofetch3 } from '#common/dofetch'\nimport { Menu, renderTable, sayerror, type TableRow, type TableColumn } from '#dom'\nimport { debounce } from 'debounce'\nimport { getCombinedTermFilter } from '#filter'\nimport { fetchBrainImagingSamples } from './getBrainImagingSampleSet.ts'\nimport svgLegend from '#dom/svg.legend'\nimport { scaleLinear } from 'd3-scale'\nimport { rgb } from 'd3-color'\n\ntype ImgData = { data: any; td: any; dataUrls: any }\n\nclass BrainImaging extends PlotBase implements RxComponent {\n\tstatic type = 'brainImaging'\n\n\ttype: string\n\tcomponents: { controls: any }\n\tlegendLabelMouseup!: any\n\timagesData!: { [index: string]: ImgData }\n\tlegendRenderer!: any\n\tlegendItems!: any\n\tlegendValues!: { [index: string]: { color: string; maxLength: number; crossedOut: boolean } }\n\tconfig!: any\n\tsettings!: any\n\tdom!: any\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = BrainImaging.type\n\t\tthis.components = { controls: {} }\n\t\tsetInteractivity(this)\n\t}\n\n\tasync init(appState) {\n\t\tconst state = this.getState(appState)\n\t\tconst holder = this.opts.holder\n\t\tif (this.opts.header) {\n\t\t\tconst fileNames = state.config.selectedSampleFileNames\n\t\t\t// show individual sample names only for small selections; otherwise show the count\n\t\t\tconst samplesLabel =\n\t\t\t\tfileNames.length < 3 ? fileNames.map(f => f.split('.nii')[0]).join(', ') : `${fileNames.length} samples`\n\t\t\tthis.opts.header\n\t\t\t\t.style('padding-left', '7px')\n\t\t\t\t.style('color', 'rgb(85, 85, 85)')\n\t\t\t\t.html(`Brain Imaging: ${state.config.queryKey}/${samplesLabel}`)\n\t\t}\n\t\tconst controlsHolder = holder.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\tconst rightDiv = holder.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\tconst headerHolder = rightDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('padding', '10px')\n\t\tconst contentHolder = rightDiv.append('div').style('vertical-align', 'top')\n\t\tconst table = contentHolder.append('table').style('border-collapse', 'collapse')\n\t\tconst headerTr = table.append('tr')\n\t\tconst contentTr = table.append('tr').style('background-color', 'black')\n\t\tconst tdL = contentTr.append('td')\n\t\tconst tdF = contentTr.append('td')\n\t\tconst tdT = contentTr.append('td')\n\t\tconst legendHolder = contentHolder.append('svg').style('width', '100%').on('mouseup', this.legendLabelMouseup)\n\t\tconst legendMenu = new Menu({ padding: '0px' })\n\n\t\tthis.dom = {\n\t\t\theaderHolder,\n\t\t\tcontentHolder,\n\t\t\theaderTr,\n\t\t\ttdL,\n\t\t\ttdF,\n\t\t\ttdT,\n\t\t\tlegendHolder,\n\t\t\tlegendMenu\n\t\t}\n\t\tthis.addSliders(state)\n\n\t\tconst configInputsOptions = this.getConfigInputsOptions(state)\n\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: controlsHolder,\n\t\t\t\tinputs: configInputsOptions\n\t\t\t})\n\t\t}\n\t\tthis.components.controls.on('downloadClick.brainImaging', () => {\n\t\t\tconst urls: unknown[] = []\n\t\t\tfor (const key in this.imagesData)\n\t\t\t\tfor (const category in this.imagesData[key].dataUrls) {\n\t\t\t\t\tconst dataUrl = this.imagesData[key].dataUrls[category].url\n\t\t\t\t\turls.push(dataUrl)\n\t\t\t\t}\n\t\t\tthis.downloadImage(urls)\n\t\t})\n\t\tthis.legendRenderer = svgLegend({ holder: this.dom.legendHolder })\n\t}\n\n\taddSliders(state) {\n\t\tconst settings = state.config.settings.brainImaging\n\t\t/* slice index ranges come from the template's voxel counts, read from the NIfTI\n\t\theader at server launch */\n\t\tconst dims = state.RefNIdata?.dimensions\n\t\tconst maxL = (dims?.l || 193) - 1\n\t\tconst maxF = (dims?.f || 229) - 1\n\t\tconst maxT = (dims?.t || 193) - 1\n\n\t\tconst tr = this.dom.headerTr\n\t\tlet td = tr.append('td')\n\t\ttd.append('label').attr('for', 'saggital').text('Sagittal:')\n\t\tthis.dom.saggitalSlider = td\n\t\t\t.append('input')\n\t\t\t.attr('id', 'saggital')\n\t\t\t.attr('type', 'range')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', maxL)\n\t\t\t.attr('value', settings.brainImageL)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageL', e.target.value)\n\t\t\t})\n\t\tthis.dom.saggitalInput = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', maxL)\n\t\t\t.attr('value', settings.brainImageL)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageL', e.target.value)\n\t\t\t})\n\t\t\t.style('vertical-align', 'top')\n\n\t\ttd = tr.append('td')\n\n\t\ttd.append('label').attr('for', 'coronal').text('Coronal:')\n\t\tthis.dom.coronalSlider = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'range')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', maxF)\n\t\t\t.attr('value', settings.brainImageF)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageF', e.target.value)\n\t\t\t})\n\t\tthis.dom.coronalInput = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', maxF)\n\t\t\t.attr('value', settings.brainImageF)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageF', e.target.value)\n\t\t\t})\n\t\t\t.style('vertical-align', 'top')\n\n\t\ttd = tr.append('td')\n\n\t\ttd.append('label').attr('for', 'axial').text('Axial:')\n\t\tthis.dom.axialSlider = td\n\t\t\t.append('input')\n\t\t\t.attr('id', 'axial')\n\t\t\t.attr('type', 'range')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', maxT)\n\t\t\t.attr('value', settings.brainImageT)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageT', e.target.value)\n\t\t\t})\n\t\tthis.dom.axialInput = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', maxT)\n\t\t\t.attr('value', settings.brainImageT)\n\t\t\t.on('change', e => {\n\t\t\t\tthis.editBrainImage('brainImageT', e.target.value)\n\t\t\t})\n\t}\n\n\teditBrainImage(key, value) {\n\t\tif (!value) return\n\t\tconst settings = { [key]: Number(value) }\n\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: { settings: { brainImaging: settings } } })\n\t}\n\n\tdownloadImage(dataUrls) {\n\t\tfor (const dataUrl of dataUrls) {\n\t\t\tconst downloadImgName = 'brainImaging'\n\t\t\tconst a = document.createElement('a')\n\t\t\tdocument.body.appendChild(a)\n\n\t\t\ta.addEventListener(\n\t\t\t\t'click',\n\t\t\t\t() => {\n\t\t\t\t\t// Download the image\n\t\t\t\t\ta.download = downloadImgName + '.png'\n\t\t\t\t\ta.href = dataUrl\n\t\t\t\t\tdocument.body.removeChild(a)\n\t\t\t\t},\n\t\t\t\tfalse\n\t\t\t)\n\t\t\ta.click()\n\t\t}\n\t}\n\n\tgetConfigInputsOptions(state) {\n\t\tif (state.config.selectedSampleFileNames.length == 1) return []\n\t\tconst mandatoryConfigInputOptions = [\n\t\t\t{\n\t\t\t\tlabel: 'Divide by',\n\t\t\t\ttype: 'term',\n\t\t\t\tchartType: 'brainImaging',\n\t\t\t\tconfigKey: 'divideByTW',\n\t\t\t\ttitle: 'Categories to divide by',\n\t\t\t\tusecase: { target: 'brainImaging', detail: 'term0' },\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\tdefaultQ4fillTW: getT0T2defaultQ()\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Color by',\n\t\t\t\ttype: 'term',\n\t\t\t\tchartType: 'brainImaging',\n\t\t\t\tconfigKey: 'overlayTW',\n\t\t\t\ttitle: 'Categories to color the samples',\n\t\t\t\tusecase: { target: 'brainImaging', detail: 'term2' },\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\tdefaultQ4fillTW: getT0T2defaultQ()\n\t\t\t}\n\t\t]\n\t\treturn mandatoryConfigInputOptions\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\n\t\t// global mass filter combined with this plot's local filter (config.filter,\n\t\t// set by the plot wrapper's filter UI); restricts which selected samples render\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter)\n\n\t\treturn {\n\t\t\tconfig,\n\t\t\ttermfilter,\n\t\t\tdslabel: appState.vocab.dslabel,\n\t\t\tgenome: appState.vocab.genome,\n\t\t\tRefNIdata: appState.termdbConfig.queries.NIdata[config.queryKey]\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = structuredClone(this.state.config) //to modify config on plot_edit\n\t\tthis.settings = this.state.config.settings.brainImaging\n\n\t\t//settings may be edited by the slider or the input, so we update the sliders and inputs to reflect the current settings\n\t\tthis.dom.saggitalSlider.property('value', this.settings.brainImageL)\n\t\tthis.dom.saggitalInput.property('value', this.settings.brainImageL)\n\t\tthis.dom.coronalSlider.property('value', this.settings.brainImageF)\n\t\tthis.dom.coronalInput.property('value', this.settings.brainImageF)\n\t\tthis.dom.axialSlider.property('value', this.settings.brainImageT)\n\t\tthis.dom.axialInput.property('value', this.settings.brainImageT)\n\n\t\tlet data\n\t\ttry {\n\t\t\tdata = await Promise.all([\n\t\t\t\tthis.requestImage('l', this.settings.brainImageL),\n\t\t\t\tthis.requestImage('f', this.settings.brainImageF),\n\t\t\t\tthis.requestImage('t', this.settings.brainImageT)\n\t\t\t])\n\t\t} catch (e: any) {\n\t\t\tthis.showNoImage(e?.message || e)\n\t\t\treturn\n\t\t}\n\t\t// e.g. none of the requested samples has an imaging file (sample view and\n\t\t// matrix may request any sample); show the message instead of crashing.\n\t\t// the route sends errors as a plain string, so it is not cached by dofetch3\n\t\tconst failedIdx = data.findIndex(d => !d || typeof d == 'string' || d.error || !d.brainImage)\n\t\tif (failedIdx != -1) {\n\t\t\tconst failed = data[failedIdx]\n\t\t\tthis.showNoImage((typeof failed == 'string' && failed) || failed?.error || 'no brain imaging data')\n\t\t\treturn\n\t\t}\n\n\t\tthis.imagesData = {\n\t\t\tbrainImageL: { dataUrls: {}, td: this.dom.tdL, data: data[0] },\n\t\t\tbrainImageF: { dataUrls: {}, td: this.dom.tdF, data: data[1] },\n\t\t\tbrainImageT: { dataUrls: {}, td: this.dom.tdT, data: data[2] }\n\t\t}\n\n\t\tfor (const img of Object.values(this.imagesData)) this.renderImages(img)\n\n\t\tthis.renderLegend()\n\t}\n\n\t// shown when image data could not be generated, e.g. the sample has no imaging file\n\tshowNoImage(message: any) {\n\t\tfor (const td of [this.dom.tdL, this.dom.tdF, this.dom.tdT]) td.selectAll('*').remove()\n\t\tthis.dom.tdL\n\t\t\t.append('div')\n\t\t\t.style('color', 'white')\n\t\t\t.style('padding', '20px')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.text(String(message))\n\t\tthis.dom.legendHolder.selectAll('*').remove()\n\t}\n\n\tasync requestImage(key, value) {\n\t\tconst body = {\n\t\t\tgenome: this.state.genome,\n\t\t\tdslabel: this.state.dslabel,\n\t\t\trefKey: this.state.config.queryKey,\n\t\t\t[key]: value,\n\t\t\tselectedSampleFileNames: this.state.config.selectedSampleFileNames,\n\t\t\tdivideByTW: this.state.config.divideByTW,\n\t\t\toverlayTW: this.state.config.overlayTW,\n\t\t\tlegendFilter: this.state.config.legendFilter,\n\t\t\tfilter: this.state.termfilter?.filter\n\t\t}\n\t\treturn await dofetch3('brainImaging', { body })\n\t}\n\n\trenderImages({ data, td, dataUrls }: ImgData) {\n\t\tthis.legendValues = data.legend\n\t\tif (data.error) throw data.error\n\t\tfor (const [termV, result] of Object.entries(data.brainImage)) {\n\t\t\tdataUrls[termV] = result\n\t\t}\n\n\t\ttd.selectAll('*').remove()\n\t\tfor (const [termV, result] of Object.entries(dataUrls)) {\n\t\t\tconst imgResult = result as { catNum: number; url: string }\n\t\t\tif (this.state.config.divideByTW)\n\t\t\t\ttd.append('div')\n\t\t\t\t\t.attr('class', 'pp-chart-title')\n\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t.text(`${termV} (n=${imgResult.catNum})`)\n\t\t\t\t\t.style('font-weight', '600')\n\t\t\t\t\t.style('color', 'white')\n\t\t\t\t\t.style('font-size', '24px')\n\t\t\t\t\t.style('margin-bottom', '5px')\n\t\t\t\t\t.style('margin-top', '5px')\n\t\t\t\t\t.style('display', 'block')\n\t\t\ttd.append('div').append('img').attr('src', imgResult.url)\n\t\t}\n\t}\n\n\trenderLegend() {\n\t\tconst legendItems: any[] = []\n\t\tfor (const [label, v] of Object.entries(this.legendValues)) {\n\t\t\tconst scale = scaleLinear([0, v.maxLength], [rgb('white').formatHex(), v.color]).clamp(true)\n\t\t\tlegendItems.push({\n\t\t\t\ttext: label == 'default' ? 'Combined Intensity' : label,\n\t\t\t\twidth: 140,\n\t\t\t\tscale,\n\t\t\t\tcolors: ['white', v.color],\n\t\t\t\tdomain: [0, v.maxLength],\n\t\t\t\tkey: label,\n\t\t\t\tcrossedOut: v.crossedOut\n\t\t\t})\n\t\t}\n\t\tthis.legendItems = legendItems\n\t\tconst legendRendererData = [\n\t\t\t{\n\t\t\t\titems: legendItems\n\t\t\t}\n\t\t]\n\n\t\tthis.legendRenderer(legendRendererData, {\n\t\t\tsettings: {\n\t\t\t\tfontsize: 16,\n\t\t\t\ticonh: 14,\n\t\t\t\ticonw: 14,\n\t\t\t\tdimensions: {\n\t\t\t\t\txOffset: 0\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n}\n\nexport function makeChartBtnMenu(holder, chartsInstance: any) {\n\tchartsInstance.dom.tip.clear()\n\tconst menuDiv = holder.append('div')\n\tif (chartsInstance.state.termdbConfig.queries.NIdata) {\n\t\t// track each template's div so that once one is chosen, the others can be hidden\n\t\tconst refDivs: any[] = []\n\t\tfor (const refKey of Object.keys(chartsInstance.state.termdbConfig.queries.NIdata)) {\n\t\t\tconst refDiv = menuDiv.append('div')\n\t\t\trefDivs.push(refDiv)\n\n\t\t\tconst refOption = refDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text(refKey)\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\t// a template is chosen: hide the other template options,\n\t\t\t\t\t// and show the chosen one as a plain label\n\t\t\t\t\tfor (const d of refDivs) if (d !== refDiv) d.style('display', 'none')\n\t\t\t\t\trefOption.attr('class', '').style('font-weight', 'bold').style('padding', '5px')\n\t\t\t\t\trefOption.on('click', null)\n\t\t\t\t\tconst body = {\n\t\t\t\t\t\tgenome: chartsInstance.opts.vocab.genome,\n\t\t\t\t\t\tdslabel: chartsInstance.opts.vocab.dslabel,\n\t\t\t\t\t\trefKey,\n\t\t\t\t\t\t// restrict the sample table by the current cohort filter, if one is set\n\t\t\t\t\t\tfilter: chartsInstance.state.filter\n\t\t\t\t\t}\n\t\t\t\t\tlet samples: any[]\n\t\t\t\t\ttry {\n\t\t\t\t\t\tconst result = await fetchBrainImagingSamples(body)\n\t\t\t\t\t\tsamples = result.samples || []\n\t\t\t\t\t} catch (e: any) {\n\t\t\t\t\t\tsayerror(refDiv, e?.message || String(e))\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\n\t\t\t\t\tconst columns = await getTableColumns(chartsInstance, refKey)\n\n\t\t\t\t\t// samples currently shown in the table (narrowed by the search box)\n\t\t\t\t\tlet shownSamples = samples\n\t\t\t\t\t// sample names checked by the user; persists across search box re-renders\n\t\t\t\t\tconst selectedSamples = new Set<string>()\n\n\t\t\t\t\t/* update selections from the checked row indexes renderTable reports;\n\t\t\t\t\tindexes point into the rows array passed to renderTable, i.e. into\n\t\t\t\t\tshownSamples, also after sorting. rows hidden by the search keep\n\t\t\t\t\ttheir recorded state, so selections persist across searches */\n\t\t\t\t\tconst updateSelections = (idxlst: number[]) => {\n\t\t\t\t\t\tconst checked = new Set(idxlst.map(i => shownSamples[i]?.sample))\n\t\t\t\t\t\tfor (const s of shownSamples) {\n\t\t\t\t\t\t\tif (!s.sample) continue\n\t\t\t\t\t\t\tif (checked.has(s.sample)) selectedSamples.add(s.sample)\n\t\t\t\t\t\t\telse selectedSamples.delete(s.sample)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\t// debounce: re-rendering a large table on every keystroke is janky\n\t\t\t\t\tconst debouncedRenderRows = debounce(() => renderRows(), 200)\n\t\t\t\t\tconst searchDiv = refDiv.append('div').style('padding', '5px 0px')\n\t\t\t\t\tconst searchInput = searchDiv\n\t\t\t\t\t\t.append('input')\n\t\t\t\t\t\t.attr('type', 'search')\n\t\t\t\t\t\t.attr('placeholder', 'Search samples')\n\t\t\t\t\t\t.style('width', '200px')\n\t\t\t\t\t\t.on('input', debouncedRenderRows)\n\t\t\t\t\tconst countLabel = searchDiv.append('span').style('margin-left', '10px').style('opacity', 0.6)\n\t\t\t\t\tconst tableDiv = refDiv.append('div')\n\n\t\t\t\t\tconst applybt = {\n\t\t\t\t\t\ttext: 'Apply',\n\t\t\t\t\t\t// unstyled button, found by testid since it carries no distinguishing class\n\t\t\t\t\t\tdataTestId: 'sjpp-brainImaging-apply',\n\t\t\t\t\t\t/* fires on every checkbox change: keeps selectedSamples current, and\n\t\t\t\t\t\toverrides the table's own disabling (which only considers visible rows)\n\t\t\t\t\t\tso Apply stays usable when checked samples are hidden by the search */\n\t\t\t\t\t\tonChange: (idxlst: number[], button: any) => {\n\t\t\t\t\t\t\tupdateSelections(idxlst)\n\t\t\t\t\t\t\tif (button) button.disabled = !selectedSamples.size\n\t\t\t\t\t\t},\n\t\t\t\t\t\tcallback: (indexes: number[]) => {\n\t\t\t\t\t\t\tupdateSelections(indexes)\n\t\t\t\t\t\t\tif (!selectedSamples.size) return\n\t\t\t\t\t\t\tchartsInstance.dom.tip.hide()\n\t\t\t\t\t\t\tconst selectedSampleFileNames = [...selectedSamples].map(s => s + '.nii')\n\t\t\t\t\t\t\t// default slice positions are resolved by getPlotConfig()\n\t\t\t\t\t\t\t// from the template's dataset-configured parameters\n\t\t\t\t\t\t\tchartsInstance.app.dispatch({\n\t\t\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\t\t\tchartType: 'brainImaging',\n\t\t\t\t\t\t\t\t\tqueryKey: refKey,\n\t\t\t\t\t\t\t\t\tselectedSampleFileNames\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\tconst renderRows = () => {\n\t\t\t\t\t\tconst str = searchInput.property('value').trim().toLowerCase()\n\t\t\t\t\t\tshownSamples = !str\n\t\t\t\t\t\t\t? samples\n\t\t\t\t\t\t\t: samples.filter(s => Object.values(s).some(v => v != undefined && String(v).toLowerCase().includes(str)))\n\t\t\t\t\t\tcountLabel.text(\n\t\t\t\t\t\t\t(str ? `${shownSamples.length} of ${samples.length} samples` : `${samples.length} samples`) +\n\t\t\t\t\t\t\t\t(selectedSamples.size ? `; ${selectedSamples.size} selected` : '')\n\t\t\t\t\t\t)\n\t\t\t\t\t\tconst rows = getTableRows(shownSamples, chartsInstance.state, refKey)\n\t\t\t\t\t\ttableDiv.selectAll('*').remove()\n\t\t\t\t\t\trenderTable({\n\t\t\t\t\t\t\trows,\n\t\t\t\t\t\t\tcolumns,\n\t\t\t\t\t\t\tresize: true,\n\t\t\t\t\t\t\tsingleMode: false,\n\t\t\t\t\t\t\tdiv: tableDiv,\n\t\t\t\t\t\t\tmaxHeight: '40vh',\n\t\t\t\t\t\t\theader: { allowSort: true },\n\t\t\t\t\t\t\tselectedRows: shownSamples.map((s, i) => (selectedSamples.has(s.sample) ? i : -1)).filter(i => i >= 0),\n\t\t\t\t\t\t\tbuttons: [applybt],\n\t\t\t\t\t\t\tbuttonsToLeft: true\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t\trenderRows()\n\t\t\t\t})\n\t\t}\n\t}\n}\n\nexport const brainImaging = getCompInit(BrainImaging)\nexport const componentInit = brainImaging\n\nexport async function getPlotConfig(opts, app) {\n\t/* default slice positions come from the template's dataset-configured\n\tparameters (NIdata[queryKey].parameters in e.g. DISCOVER.hg38.ts); a ds\n\tthat omits parameters falls back to the volume midpoint (dimensions are\n\tread from the NIfTI header at server launch), then to default numbers */\n\tconst ref = app.vocabApi?.termdbConfig?.queries?.NIdata?.[opts.queryKey]\n\tconst parameters = ref?.parameters\n\tconst dims = ref?.dimensions\n\tconst settings = {\n\t\tbrainImaging: {\n\t\t\tbrainImageL: parameters?.l ?? (dims ? Math.floor(dims.l / 2) : 98),\n\t\t\tbrainImageF: parameters?.f ?? (dims ? Math.floor(dims.f / 2) : 81),\n\t\t\tbrainImageT: parameters?.t ?? (dims ? Math.floor(dims.t / 2) : 53)\n\t\t}\n\t}\n\tconst config: any = { chartType: 'brainImaging', settings }\n\tcopyMerge(config, opts)\n\t/* a tw of a saved session is only raw until it is filled here, same as every other\n\tchart type. required, since a session is serialized without the derived properties\n\tof a geneVariant term, see trimGvTermsForSave() */\n\tif (config.overlayTW) config.overlayTW = await fillTermWrapper(config.overlayTW, app.vocabApi)\n\tif (config.divideByTW) config.divideByTW = await fillTermWrapper(config.divideByTW, app.vocabApi)\n\treturn config\n}\n\nfunction getTableRows(samples, state, refKey): TableRow[] {\n\tconst rows: TableRow[] = []\n\tfor (const sample of samples) {\n\t\t// first cell is sample name\n\t\tconst row = [{ value: sample.sample }]\n\n\t\t// optional sample columns\n\t\tfor (const c of state.termdbConfig.queries.NIdata[refKey].sampleColumns || []) {\n\t\t\trow.push({ value: sample[c.termid] })\n\t\t}\n\t\trows.push(row)\n\t}\n\treturn rows\n}\n\nasync function getTableColumns(self, refKey): Promise<TableColumn[]> {\n\t// first column is sample and is hardcoded\n\tconst columns: TableColumn[] = [{ label: 'Sample', sortable: true }]\n\n\t// add in optional sample columns\n\tfor (const c of self.state.termdbConfig.queries.NIdata[refKey].sampleColumns || []) {\n\t\tcolumns.push({\n\t\t\tlabel: (await self.app.vocabApi.getterm(c.termid)).name,\n\t\t\tsortable: true\n\t\t})\n\t}\n\n\treturn columns\n}\n\nfunction setInteractivity(self) {\n\tself.legendLabelMouseup = event => {\n\t\tconst targetData = event.target.__data__\n\t\tif (!targetData || targetData.key == 'default') return\n\t\tconst legendMenu = self.dom.legendMenu.clear()\n\t\tconst legendMenuDiv = legendMenu.d.append('div')\n\t\tconst legendFilter = self.state.config.legendFilter ? [...self.state.config.legendFilter] : []\n\n\t\tconst legendFilterIndex = legendFilter.indexOf(targetData.key)\n\n\t\tif (legendFilterIndex !== -1 || legendFilter.length + 1 !== self.legendItems.length) {\n\t\t\t// only show the Hide option when the cat is not the last shown cat\n\t\t\tlegendMenuDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text(legendFilterIndex == -1 ? 'Hide' : 'Show')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tlegendMenu.hide()\n\t\t\t\t\tif (legendFilterIndex == -1) legendFilter.push(targetData.key)\n\t\t\t\t\telse legendFilter.splice(legendFilterIndex, 1)\n\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\tconfig: { legendFilter }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\n\t\tlegendMenuDiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text('Show only')\n\t\t\t.on('click', () => {\n\t\t\t\tlegendMenu.hide()\n\t\t\t\tconst legendFilter: unknown[] = []\n\t\t\t\tfor (const legendCat of self.legendItems) {\n\t\t\t\t\tif (legendCat.key !== targetData.key) legendFilter.push(legendCat.key)\n\t\t\t\t}\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: { legendFilter }\n\t\t\t\t})\n\t\t\t})\n\n\t\tlegendMenuDiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text('Show all')\n\t\t\t.on('click', () => {\n\t\t\t\tlegendMenu.hide()\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: { legendFilter: [] }\n\t\t\t\t})\n\t\t\t})\n\n\t\t//TODO: support changing color for grouped geneVariant term\n\t\tif (self.state.config.overlayTW.term.type != 'geneVariant') {\n\t\t\tlet color = self.state.config.overlayTW?.term?.values?.[targetData.key]?.color || 'red'\n\t\t\tcolor = rgb(color).formatHex() //so that the color is in the correct format to be shown in the input\n\t\t\tlegendMenuDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '0px 10px')\n\t\t\t\t.text('Color:')\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.attr('value', color)\n\t\t\t\t.on('change', e => {\n\t\t\t\t\tself.changeColor(targetData.key, e.target.value)\n\t\t\t\t})\n\t\t}\n\t\tlegendMenu.showunder(event.target)\n\t}\n\n\tself.changeColor = async function (key, color) {\n\t\tconst tw = self.config.overlayTW\n\n\t\tif (!(tw.term.type == 'geneVariant' && tw.q.type == 'values') && tw.term.values[key])\n\t\t\ttw.term.values[key].color = color\n\t\telse {\n\t\t\tif (!tw.term.values) tw.term.values = {}\n\t\t\tif (!tw.term.values[key]) tw.term.values[key] = {}\n\t\t\ttw.term.values[key].color = color\n\t\t}\n\n\t\tawait self.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: { overlayTW: tw }\n\t\t})\n\t}\n}\n"],
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