@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

package/dist/proteinView-LWVWJY54.js

@@ -0,0 +1,444 @@
+import {
+  toTvslstFilter
+} from "./chunk-HWHG63LH.js";
+import {
+  LegendCircleReference,
+  PlotBase,
+  addGeneSearchbox,
+  axisstyle,
+  table2col
+} from "./chunk-NVB7MQLH.js";
+import {
+  aa2gmcoord
+} from "./chunk-HJ6L54YS.js";
+import "./chunk-4JON7TLI.js";
+import {
+  dofetch3
+} from "./chunk-7RN3L2BX.js";
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import {
+  roundValue
+} from "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import {
+  NumericModes,
+  TermTypes
+} from "./chunk-6ITDJ5UR.js";
+import {
+  getColors,
+  mclass
+} from "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import {
+  axisBottom,
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import {
+  linear
+} from "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import {
+  rgb
+} from "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/proteinView.ts
+var defaultConfig = {
+  chartType: "proteinView"
+};
+var ProteinView = class _ProteinView extends PlotBase {
+  static {
+    this.type = "proteinView";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _ProteinView.type;
+    this.components = {};
+  }
+  async init() {
+    const holder = this.opts.holder.append("div").style("padding", "10px");
+    this.dom = {
+      holder,
+      body: holder.append("div"),
+      tip: new Menu({ padding: "" })
+    };
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) throw `No plot with id='${this.id}' found`;
+    return { config };
+  }
+  async main() {
+    const term = this.state.config?.tw?.term;
+    if (!term?.name) throw new Error("proteinView: selected protein term is missing");
+    const body = {
+      genome: this.app.opts.state.vocab.genome,
+      dslabel: this.app.opts.state.vocab.dslabel,
+      term: this.state.config.tw,
+      filter: this.state.config.filter,
+      filter0: this.state.config.filter0
+    };
+    const data = await dofetch3("termdb/proteome", { body });
+    if (data.error) throw data.error;
+    this.dom.body.selectAll("*").remove();
+    renderCohortVolcano(this.dom.body, data, this);
+    renderPTMLollipop(this.dom.body, data, this);
+  }
+};
+function renderCohortVolcano(holder, data, self) {
+  const dots = [];
+  for (const cohortData of data?.cohorts || []) {
+    const log2fc = getLog2Ratio(cohortData.foldChange);
+    const pValue = Number(cohortData.pValue);
+    const testedN = Number(cohortData.testedN);
+    const controlN = Number(cohortData.controlN);
+    if (log2fc === null || !Number.isFinite(pValue) || pValue <= 0) continue;
+    dots.push({
+      assayName: cohortData.assayName,
+      cohortName: cohortData.cohortName,
+      PTMType: cohortData.PTMType,
+      modSites: cohortData.modSites,
+      proteinAccession: cohortData.proteinAccession,
+      uniqueIdentifier: cohortData.uniqueIdentifier,
+      log2fc,
+      pValue,
+      score: -Math.log10(Math.max(pValue, 1e-300)),
+      testedN: Number.isFinite(testedN) ? testedN : 0,
+      controlN: Number.isFinite(controlN) ? controlN : 0
+    });
+  }
+  const panel = holder.append("div").style("margin-bottom", "14px");
+  panel.append("div").style("font-weight", 600).style("margin-bottom", "6px").text("Cohort Volcano");
+  if (!dots.length) {
+    panel.append("div").style("font-size", ".85em").style("color", "#666").text("No cohorts with valid fold-change and p-value to plot.");
+    return;
+  }
+  const width = 640;
+  const height = 660;
+  const margin = { top: 40, right: 70, bottom: 120, left: 70 };
+  const innerW = width - margin.left - margin.right;
+  const innerH = height - margin.top - margin.bottom;
+  let minX = Number.POSITIVE_INFINITY;
+  let maxX = Number.NEGATIVE_INFINITY;
+  let maxY = 0;
+  let maxTestedN = 0;
+  let minTestedN = Number.POSITIVE_INFINITY;
+  for (const p of dots) {
+    minX = Math.min(minX, p.log2fc);
+    maxX = Math.max(maxX, p.log2fc);
+    maxY = Math.max(maxY, p.score);
+    maxTestedN = Math.max(maxTestedN, p.testedN);
+    if (p.testedN > 0) minTestedN = Math.min(minTestedN, p.testedN);
+  }
+  if (maxY < 1) maxY = 1;
+  if (!Number.isFinite(minTestedN)) minTestedN = 1;
+  const xSpan = Math.max(0.05, maxX - minX);
+  const xPad = Math.max(0.01, xSpan * 0.1);
+  const xMin = Math.min(0, minX - xPad);
+  const xMax = Math.max(0, maxX + xPad);
+  const yMax = maxY * 1.15;
+  const xScale = linear().domain([xMin, xMax]).range([0, innerW]);
+  const yScale = linear().domain([0, yMax]).range([innerH, 0]);
+  const radiusScale = linear().domain([minTestedN, Math.max(minTestedN + 1, maxTestedN)]).range([4, 12]);
+  const assayNames = [...new Set(dots.map((d) => d.assayName))].sort();
+  const cohortNames = [...new Set(dots.map((d) => d.cohortName))].sort();
+  const proteinAccessions = [...new Set(dots.map((d) => d.proteinAccession))].sort();
+  const assayColorScale = getColors(assayNames.length).domain(assayNames);
+  const cohortColorScale = getColors(cohortNames.length).domain(cohortNames);
+  const proteinColorScale = getColors(proteinAccessions.length).domain(proteinAccessions);
+  const assayColors = new Map(assayNames.map((name) => [name, rgb(assayColorScale(name)).formatHex()]));
+  const cohortColors = new Map(cohortNames.map((name) => [name, rgb(cohortColorScale(name)).formatHex()]));
+  const proteinColors = new Map(
+    proteinAccessions.map((acc) => [acc, rgb(proteinColorScale(acc)).formatHex()])
+  );
+  let colorMode = "assayType";
+  const getColor = (d) => {
+    switch (colorMode) {
+      case "assayType":
+        return assayColors.get(d.assayName) ?? "#888";
+      case "cohort":
+        return cohortColors.get(d.cohortName) ?? "#888";
+      case "proteinAccession":
+        return proteinColors.get(d.proteinAccession) ?? "#888";
+      default:
+        return "#888";
+    }
+  };
+  const plotAndLegend = panel.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "14px").style("flex-wrap", "wrap");
+  const svg = plotAndLegend.append("svg").attr("width", width).attr("height", height).style("display", "block").style("max-width", "100%").style("height", "auto");
+  const g = svg.append("g").attr("transform", `translate(${margin.left},${margin.top})`);
+  const xAxis = g.append("g").attr("transform", `translate(0,${innerH})`).call(axisBottom(xScale));
+  axisstyle({ axis: xAxis, color: "black", showline: true });
+  const yAxis = g.append("g").call(axisLeft(yScale));
+  axisstyle({ axis: yAxis, color: "black", showline: true });
+  const x0 = xScale(0);
+  const pThreshold = -Math.log10(0.05);
+  const thresholdY = yScale(Math.min(yMax, pThreshold));
+  g.append("line").attr("x1", x0).attr("x2", x0).attr("y1", 0).attr("y2", innerH).attr("stroke", "black").attr("stroke-dasharray", "5 4").attr("stroke-opacity", 0.4);
+  g.append("line").attr("x1", 0).attr("x2", innerW).attr("y1", thresholdY).attr("y2", thresholdY).attr("stroke", "black").attr("stroke-dasharray", "5 4").attr("stroke-opacity", 0.4);
+  g.append("text").attr("x", innerW / 2).attr("y", innerH + 44).attr("text-anchor", "middle").style("font-weight", 600).text("log2 fold change (disease / control)");
+  g.append("text").attr("transform", `translate(${-50},${innerH / 2}) rotate(-90)`).attr("text-anchor", "middle").style("font-weight", 600).text("-log10(p-value)");
+  const cohortDots = g.selectAll("circle.cohort-dot").data(dots).enter().append("circle").attr("class", "cohort-dot").attr("cx", (d) => xScale(d.log2fc)).attr("cy", (d) => yScale(d.score)).attr("r", (d) => radiusScale(Math.max(minTestedN, d.testedN || minTestedN)) * 0.9).attr("fill", (d) => getColor(d)).attr("fill-opacity", 0.5).attr("stroke", (d) => getColor(d)).attr("stroke-width", 1).style("cursor", "pointer");
+  cohortDots.transition().duration(350).attr("r", (d) => radiusScale(Math.max(minTestedN, d.testedN || minTestedN))).attr("cx", (d) => xScale(d.log2fc)).attr("cy", (d) => yScale(d.score));
+  cohortDots.on("mouseover", function(_event, d) {
+    self.dom.tip.clear().showunder(this);
+    const table = table2col({ holder: self.dom.tip.d.append("table") });
+    table.addRow("Assay", d.assayName);
+    table.addRow("Cohort", d.cohortName);
+    table.addRow("Protein Accession", d.proteinAccession);
+    if (d.PTMType) {
+      table.addRow("PTM Type", d.PTMType);
+      table.addRow("Modified Site", d.modSites);
+      table.addRow("PTM", d.uniqueIdentifier);
+    } else table.addRow("Isoform", d.uniqueIdentifier);
+    table.addRow("log2 fold change", roundValue(d.log2fc, 3));
+    table.addRow("p value", d.pValue.toExponential(2));
+    table.addRow("-log10(p)", roundValue(d.score, 3));
+    table.addRow("Tested samples", d.testedN);
+    table.addRow("Control samples", d.controlN);
+  }).on("mouseout", () => {
+    self.dom.tip.hide();
+  }).on("click", (_event, d) => launchViolinPlot(self, d.assayName, d.cohortName, d.uniqueIdentifier));
+  const legend = plotAndLegend.append("div").style("margin", "0").style("min-width", "220px").style("font-size", ".75em").style("color", "#374151");
+  const colorLegendDiv = legend.append("div").style("margin-bottom", "12px");
+  function renderColorLegend() {
+    colorLegendDiv.selectAll("*").remove();
+    const modeRow = colorLegendDiv.append("div").style("display", "flex").style("gap", "10px").style("margin-bottom", "6px").style("flex-wrap", "wrap");
+    modeRow.append("span").text("Color by");
+    const modes = [
+      { key: "assayType", label: "Assay" },
+      { key: "cohort", label: "Cohort" },
+      { key: "proteinAccession", label: "Isoform" }
+    ];
+    for (const { key, label } of modes) {
+      modeRow.append("span").text(label).style("cursor", "pointer").style("font-weight", key === colorMode ? "600" : "400").style("text-decoration", key === colorMode ? "underline" : "none").style("color", key === colorMode ? "#111" : "#6b7280").on("click", () => {
+        colorMode = key;
+        cohortDots.attr("fill", (d) => getColor(d)).attr("stroke", (d) => getColor(d));
+        renderColorLegend();
+      });
+    }
+    const makeLegendItems = (items, colorMap) => {
+      for (const name of items) {
+        const row = colorLegendDiv.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px").style("margin-bottom", "3px");
+        const swatch = row.append("span").style("display", "inline-block").style("width", "10px").style("height", "10px").style("border-radius", "50%").style("background", colorMap.get(name) ?? "#888").style("opacity", 0.8).style("flex-shrink", "0").style("cursor", "pointer");
+        swatch.on("click", (event) => {
+          const menu = new Menu({ padding: "0px" });
+          const div = menu.d.append("div");
+          const input = div.append("div").attr("class", "sja_sharp_border").style("padding", "0px 10px").text("Color:").append("input").attr("type", "color").attr("value", colorMap.get(name) ?? "#888").on("change", () => {
+            const newColor = input.node().value;
+            colorMap.set(name, newColor);
+            swatch.style("background", newColor);
+            cohortDots.attr("fill", (d) => getColor(d)).attr("stroke", (d) => getColor(d));
+            menu.hide();
+          });
+          menu.showunder(event.target);
+        });
+        row.append("span").text(name);
+      }
+    };
+    if (colorMode === "assayType") {
+      makeLegendItems(assayNames, assayColors);
+    } else if (colorMode === "cohort") {
+      makeLegendItems(cohortNames, cohortColors);
+    } else if (colorMode === "proteinAccession") {
+      makeLegendItems(proteinAccessions, proteinColors);
+    }
+  }
+  renderColorLegend();
+  const sizeLegendRow = legend.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "8px").style("margin-top", "8px");
+  sizeLegendRow.append("span").style("display", "inline-block").style("margin-top", "42px").text("Tested sample size");
+  const legendSvg = sizeLegendRow.append("svg").attr("width", 190).attr("height", 110).style("display", "block");
+  new LegendCircleReference({
+    g: legendSvg.append("g").attr("transform", "translate(12, 8)"),
+    inputMax: 12,
+    inputMin: 4,
+    maxLabel: maxTestedN || minTestedN,
+    maxRadius: radiusScale(Math.max(minTestedN + 1, maxTestedN || minTestedN)),
+    minLabel: minTestedN,
+    minRadius: radiusScale(minTestedN),
+    title: "",
+    menu: {
+      minMaxLabel: "pixels",
+      callback: async () => {
+      }
+    }
+  });
+}
+function launchViolinPlot(self, assayName, cohortName, isoForm) {
+  const selectedProtein = self.state.config?.tw?.term;
+  if (!selectedProtein) throw new Error("proteinView: selected protein term is missing");
+  const action = {
+    type: "plot_create",
+    config: {
+      chartType: "summary"
+    }
+  };
+  action.config.assayCohortTitle = `${assayName}: ${cohortName}`;
+  action.config.proteomeDetails = { assay: assayName, cohort: cohortName };
+  const termdbConfig = self.app.vocabApi.termdbConfig;
+  const cohortSelected = termdbConfig?.queries?.proteome?.assays?.[assayName]?.cohorts?.[cohortName];
+  if (cohortSelected?.filter) action.config.filter = toTvslstFilter(cohortSelected.filter);
+  const t = structuredClone(selectedProtein);
+  t.name = `${t.name}: ${isoForm}`;
+  t.proteomeDetails = { assay: assayName, cohort: cohortName };
+  action.config.term = { term: t, q: { mode: NumericModes.continuous } };
+  if (cohortSelected?.overlayTerm) {
+    action.config.term2 = { term: structuredClone(cohortSelected.overlayTerm), q: {} };
+  }
+  self.app.dispatch(action);
+}
+async function renderPTMLollipop(holder, data, self) {
+  if (!data?.cohorts?.length) return;
+  const custom_variants = [];
+  const mergedMclassOverride = {};
+  const gmCache = /* @__PURE__ */ new Map();
+  for (const ptm of data.cohorts) {
+    if (!ptm.PTMType) continue;
+    const gm = await getGmForPTM(ptm.geneName, self.app.opts.genome.name, gmCache);
+    if (!gm) continue;
+    const logValue = getLog2Ratio(ptm.foldChange);
+    if (ptm.mclassOverride && typeof ptm.mclassOverride == "object") {
+      Object.assign(mergedMclassOverride, ptm.mclassOverride);
+    }
+    const site = parsePTMModSites(ptm.modSites);
+    if (!site) continue;
+    const pos = aa2gmcoord(site, gm);
+    if (!Number.isInteger(pos)) continue;
+    const ptmClass = Object.keys(ptm.mclassOverride || {})[0];
+    custom_variants.push({
+      chr: gm.chr,
+      pos,
+      mname: `${ptm.modSites}: ${ptm.cohortName}`,
+      class: ptmClass,
+      dt: 1,
+      logValue
+    });
+  }
+  if (!custom_variants.length) return;
+  const mclassOverride = {
+    className: "PTMs",
+    classes: mergedMclassOverride
+  };
+  for (const key in mclassOverride.classes) {
+    if (mclass[key]) Object.assign(mclass[key], mclassOverride.classes[key]);
+  }
+  const tk = {
+    type: "mds3",
+    name: "PTMs",
+    custom_variants,
+    skewerModes: [
+      {
+        type: "numeric",
+        byAttribute: "logValue",
+        label: "Log2FC Disease vs Control",
+        inuse: true,
+        axisheight: 100
+      }
+    ],
+    mclassOverride
+  };
+  const arg = {
+    holder: holder.append("div"),
+    genome: self.app.opts.genome,
+    nobox: true,
+    tklst: [tk],
+    mclassOverride,
+    debugmode: self.app.opts.debug,
+    query: data.cohorts[0].geneName
+  };
+  const _ = await import("./block.init-7J5OHYKA.js");
+  await _.default(arg);
+}
+function parsePTMModSites(modSites) {
+  if (!modSites) return null;
+  const regex = /([A-Za-z])(\d+)/g;
+  let m;
+  while ((m = regex.exec(modSites)) !== null) {
+    const position = Number(m[2]);
+    if (!Number.isInteger(position) || position < 1) continue;
+    return position;
+  }
+  return null;
+}
+async function getGmForPTM(geneName, genomeName, gmCache) {
+  if (!geneName) return null;
+  if (gmCache.has(geneName)) return gmCache.get(geneName);
+  const d = await dofetch3("genelookup", {
+    body: {
+      deep: 1,
+      genome: genomeName,
+      input: geneName
+    }
+  });
+  if (d.error || !Array.isArray(d.gmlst) || !d.gmlst.length) {
+    gmCache.set(geneName, null);
+    return null;
+  }
+  const gm = d.gmlst.find((i) => i.isdefault) || d.gmlst[0];
+  gmCache.set(geneName, gm);
+  return gm;
+}
+function getLog2Ratio(foldChange) {
+  if (!Number.isFinite(foldChange) || foldChange <= 0) return null;
+  return Math.log2(foldChange);
+}
+async function getPlotConfig(opts) {
+  const config = structuredClone(defaultConfig);
+  if (!opts.tw) throw new Error("proteinView requires opts.tw");
+  return copyMerge(config, opts);
+}
+function makeChartBtnMenu(holder, chartsInstance) {
+  const row = holder.append("div").style("padding", "5px");
+  row.append("span").style("font-weight", "bold").text("Enter a gene name:");
+  const geneSearch = addGeneSearchbox({
+    row,
+    genome: chartsInstance.app.opts.genome,
+    tip: new Menu({ padding: "0px" }),
+    searchOnly: "gene",
+    callback: async () => {
+      if (!geneSearch.geneSymbol) throw new Error("A valid gene selection is required");
+      chartsInstance.dom.tip.hide();
+      chartsInstance.app.dispatch({
+        type: "plot_create",
+        config: {
+          chartType: "proteinView",
+          tw: {
+            term: {
+              gene: geneSearch.geneSymbol,
+              name: geneSearch.geneSymbol,
+              type: TermTypes.PROTEOME_ABUNDANCE
+            }
+          }
+        }
+      });
+    }
+  });
+}
+var proteinViewInit = getCompInit(ProteinView);
+var componentInit = proteinViewInit;
+export {
+  componentInit,
+  getPlotConfig,
+  makeChartBtnMenu,
+  proteinViewInit
+};
+//# sourceMappingURL=proteinView-LWVWJY54.js.map

package/dist/proteinView-LWVWJY54.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/proteinView.ts"],
+  "sourcesContent": ["import type { MassState, BasePlotConfig } from '#mass/types/mass'\nimport { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { axisstyle } from '#src/client'\nimport { Menu, table2col, LegendCircleReference, addGeneSearchbox } from '#dom'\nimport { PlotBase } from './PlotBase'\nimport { dofetch3 } from '#common/dofetch'\nimport { axisBottom, axisLeft } from 'd3-axis'\nimport { scaleLinear } from 'd3-scale'\nimport { rgb } from 'd3-color'\nimport { NumericModes, TermTypes } from '#shared/terms.js'\nimport { toTvslstFilter } from './proteomeAbundance.js'\nimport { aa2gmcoord } from '#src/coord'\nimport { mclass, getColors } from '#shared/common.js'\nimport { roundValue } from '#shared/roundValue.js'\n\nconst defaultConfig = {\n\tchartType: 'proteinView'\n}\n\nclass ProteinView extends PlotBase implements RxComponent {\n\tstatic type = 'proteinView'\n\ttype: string\n\tdom!: {\n\t\tholder: any\n\t\tbody: any\n\t\ttip: Menu\n\t}\n\tcomponents: any\n\n\tconstructor(opts: any, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = ProteinView.type\n\t\tthis.components = {}\n\t}\n\n\tasync init() {\n\t\tconst holder = this.opts.holder.append('div').style('padding', '10px')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tbody: holder.append('div'),\n\t\t\ttip: new Menu({ padding: '' })\n\t\t}\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config: any = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn { config }\n\t}\n\n\tasync main() {\n\t\tconst term = this.state.config?.tw?.term\n\t\tif (!term?.name) throw new Error('proteinView: selected protein term is missing')\n\n\t\tconst body = {\n\t\t\tgenome: this.app.opts.state.vocab.genome,\n\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\tterm: this.state.config.tw,\n\t\t\tfilter: this.state.config.filter,\n\t\t\tfilter0: this.state.config.filter0\n\t\t}\n\n\t\tconst data = await dofetch3('termdb/proteome', { body })\n\t\tif (data.error) throw data.error\n\t\tthis.dom.body.selectAll('*').remove()\n\t\trenderCohortVolcano(this.dom.body, data, this)\n\t\trenderPTMLollipop(this.dom.body, data, this)\n\t}\n}\n\nfunction renderCohortVolcano(holder: any, data: any, self: ProteinView) {\n\tconst dots: any[] = []\n\n\tfor (const cohortData of data?.cohorts || []) {\n\t\tconst log2fc = getLog2Ratio(cohortData.foldChange)\n\t\tconst pValue = Number(cohortData.pValue)\n\t\tconst testedN = Number(cohortData.testedN)\n\t\tconst controlN = Number(cohortData.controlN)\n\t\tif (log2fc === null || !Number.isFinite(pValue) || pValue <= 0) continue\n\t\tdots.push({\n\t\t\tassayName: cohortData.assayName,\n\t\t\tcohortName: cohortData.cohortName,\n\t\t\tPTMType: cohortData.PTMType,\n\t\t\tmodSites: cohortData.modSites,\n\t\t\tproteinAccession: cohortData.proteinAccession,\n\t\t\tuniqueIdentifier: cohortData.uniqueIdentifier,\n\t\t\tlog2fc,\n\t\t\tpValue,\n\t\t\tscore: -Math.log10(Math.max(pValue, 1e-300)),\n\t\t\ttestedN: Number.isFinite(testedN) ? testedN : 0,\n\t\t\tcontrolN: Number.isFinite(controlN) ? controlN : 0\n\t\t})\n\t}\n\n\tconst panel = holder.append('div').style('margin-bottom', '14px')\n\tpanel.append('div').style('font-weight', 600).style('margin-bottom', '6px').text('Cohort Volcano')\n\n\tif (!dots.length) {\n\t\tpanel\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.85em')\n\t\t\t.style('color', '#666')\n\t\t\t.text('No cohorts with valid fold-change and p-value to plot.')\n\t\treturn\n\t}\n\n\tconst width = 640\n\tconst height = 660\n\tconst margin = { top: 40, right: 70, bottom: 120, left: 70 }\n\tconst innerW = width - margin.left - margin.right\n\tconst innerH = height - margin.top - margin.bottom\n\n\tlet minX = Number.POSITIVE_INFINITY\n\tlet maxX = Number.NEGATIVE_INFINITY\n\tlet maxY = 0\n\tlet maxTestedN = 0\n\tlet minTestedN = Number.POSITIVE_INFINITY\n\tfor (const p of dots) {\n\t\tminX = Math.min(minX, p.log2fc)\n\t\tmaxX = Math.max(maxX, p.log2fc)\n\t\tmaxY = Math.max(maxY, p.score)\n\t\tmaxTestedN = Math.max(maxTestedN, p.testedN)\n\t\tif (p.testedN > 0) minTestedN = Math.min(minTestedN, p.testedN)\n\t}\n\n\tif (maxY < 1) maxY = 1\n\tif (!Number.isFinite(minTestedN)) minTestedN = 1\n\n\tconst xSpan = Math.max(0.05, maxX - minX)\n\tconst xPad = Math.max(0.01, xSpan * 0.1)\n\tconst xMin = Math.min(0, minX - xPad)\n\tconst xMax = Math.max(0, maxX + xPad)\n\tconst yMax = maxY * 1.15\n\n\tconst xScale = scaleLinear().domain([xMin, xMax]).range([0, innerW])\n\tconst yScale = scaleLinear().domain([0, yMax]).range([innerH, 0])\n\tconst radiusScale = scaleLinear()\n\t\t.domain([minTestedN, Math.max(minTestedN + 1, maxTestedN)])\n\t\t.range([4, 12])\n\n\tconst assayNames = [...new Set(dots.map((d: any) => d.assayName))].sort() as string[]\n\tconst cohortNames = [...new Set(dots.map((d: any) => d.cohortName))].sort() as string[]\n\tconst proteinAccessions = [...new Set(dots.map((d: any) => d.proteinAccession))].sort() as string[]\n\n\t// Create color scales for each grouping category\n\tconst assayColorScale = getColors(assayNames.length).domain(assayNames)\n\tconst cohortColorScale = getColors(cohortNames.length).domain(cohortNames)\n\tconst proteinColorScale = getColors(proteinAccessions.length).domain(proteinAccessions)\n\n\t// Store colors in maps\n\tconst assayColors = new Map<string, string>(assayNames.map(name => [name, rgb(assayColorScale(name)).formatHex()]))\n\tconst cohortColors = new Map<string, string>(cohortNames.map(name => [name, rgb(cohortColorScale(name)).formatHex()]))\n\tconst proteinColors = new Map<string, string>(\n\t\tproteinAccessions.map(acc => [acc, rgb(proteinColorScale(acc)).formatHex()])\n\t)\n\n\tlet colorMode: 'assayType' | 'cohort' | 'proteinAccession' = 'assayType'\n\tconst getColor = (d: any) => {\n\t\tswitch (colorMode) {\n\t\t\tcase 'assayType':\n\t\t\t\treturn assayColors.get(d.assayName) ?? '#888'\n\t\t\tcase 'cohort':\n\t\t\t\treturn cohortColors.get(d.cohortName) ?? '#888'\n\t\t\tcase 'proteinAccession':\n\t\t\t\treturn proteinColors.get(d.proteinAccession) ?? '#888'\n\t\t\tdefault:\n\t\t\t\treturn '#888'\n\t\t}\n\t}\n\n\tconst plotAndLegend = panel\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'flex-start')\n\t\t.style('gap', '14px')\n\t\t.style('flex-wrap', 'wrap')\n\n\tconst svg = plotAndLegend\n\t\t.append('svg')\n\t\t.attr('width', width)\n\t\t.attr('height', height)\n\t\t.style('display', 'block')\n\t\t.style('max-width', '100%')\n\t\t.style('height', 'auto')\n\tconst g = svg.append('g').attr('transform', `translate(${margin.left},${margin.top})`)\n\n\tconst xAxis = g.append('g').attr('transform', `translate(0,${innerH})`).call(axisBottom(xScale))\n\taxisstyle({ axis: xAxis, color: 'black', showline: true })\n\n\tconst yAxis = g.append('g').call(axisLeft(yScale))\n\taxisstyle({ axis: yAxis, color: 'black', showline: true })\n\n\tconst x0 = xScale(0)\n\tconst pThreshold = -Math.log10(0.05)\n\tconst thresholdY = yScale(Math.min(yMax, pThreshold))\n\n\t// Guide lines\n\tg.append('line')\n\t\t.attr('x1', x0)\n\t\t.attr('x2', x0)\n\t\t.attr('y1', 0)\n\t\t.attr('y2', innerH)\n\t\t.attr('stroke', 'black')\n\t\t.attr('stroke-dasharray', '5 4')\n\t\t.attr('stroke-opacity', 0.4)\n\n\tg.append('line')\n\t\t.attr('x1', 0)\n\t\t.attr('x2', innerW)\n\t\t.attr('y1', thresholdY)\n\t\t.attr('y2', thresholdY)\n\t\t.attr('stroke', 'black')\n\t\t.attr('stroke-dasharray', '5 4')\n\t\t.attr('stroke-opacity', 0.4)\n\n\t// Axis labels\n\tg.append('text')\n\t\t.attr('x', innerW / 2)\n\t\t.attr('y', innerH + 44)\n\t\t.attr('text-anchor', 'middle')\n\t\t.style('font-weight', 600)\n\t\t.text('log2 fold change (disease / control)')\n\n\tg.append('text')\n\t\t.attr('transform', `translate(${-50},${innerH / 2}) rotate(-90)`)\n\t\t.attr('text-anchor', 'middle')\n\t\t.style('font-weight', 600)\n\t\t.text('-log10(p-value)')\n\n\t// Points\n\tconst cohortDots = g\n\t\t.selectAll('circle.cohort-dot')\n\t\t.data(dots)\n\t\t.enter()\n\t\t.append('circle')\n\t\t.attr('class', 'cohort-dot')\n\t\t.attr('cx', (d: any) => xScale(d.log2fc))\n\t\t.attr('cy', (d: any) => yScale(d.score))\n\t\t.attr('r', (d: any) => radiusScale(Math.max(minTestedN, d.testedN || minTestedN)) * 0.9)\n\t\t.attr('fill', (d: any) => getColor(d))\n\t\t.attr('fill-opacity', 0.5)\n\t\t.attr('stroke', (d: any) => getColor(d))\n\t\t.attr('stroke-width', 1)\n\t\t.style('cursor', 'pointer')\n\n\tcohortDots\n\t\t.transition()\n\t\t.duration(350)\n\t\t.attr('r', (d: any) => radiusScale(Math.max(minTestedN, d.testedN || minTestedN)))\n\t\t.attr('cx', (d: any) => xScale(d.log2fc))\n\t\t.attr('cy', (d: any) => yScale(d.score))\n\n\tcohortDots\n\t\t.on('mouseover', function (this: any, _event: any, d: any) {\n\t\t\tself.dom.tip.clear().showunder(this)\n\t\t\tconst table = table2col({ holder: self.dom.tip.d.append('table') })\n\t\t\ttable.addRow('Assay', d.assayName)\n\t\t\ttable.addRow('Cohort', d.cohortName)\n\t\t\ttable.addRow('Protein Accession', d.proteinAccession)\n\t\t\tif (d.PTMType) {\n\t\t\t\ttable.addRow('PTM Type', d.PTMType)\n\t\t\t\ttable.addRow('Modified Site', d.modSites)\n\t\t\t\ttable.addRow('PTM', d.uniqueIdentifier)\n\t\t\t} else table.addRow('Isoform', d.uniqueIdentifier)\n\t\t\ttable.addRow('log2 fold change', roundValue(d.log2fc, 3))\n\t\t\ttable.addRow('p value', d.pValue.toExponential(2))\n\t\t\ttable.addRow('-log10(p)', roundValue(d.score, 3))\n\t\t\ttable.addRow('Tested samples', d.testedN)\n\t\t\ttable.addRow('Control samples', d.controlN)\n\t\t})\n\t\t.on('mouseout', () => {\n\t\t\tself.dom.tip.hide()\n\t\t})\n\t\t.on('click', (_event: any, d: any) => launchViolinPlot(self, d.assayName, d.cohortName, d.uniqueIdentifier))\n\n\tconst legend = plotAndLegend\n\t\t.append('div')\n\t\t.style('margin', '0')\n\t\t.style('min-width', '220px')\n\t\t.style('font-size', '.75em')\n\t\t.style('color', '#374151')\n\n\tconst colorLegendDiv = legend.append('div').style('margin-bottom', '12px')\n\n\tfunction renderColorLegend() {\n\t\tcolorLegendDiv.selectAll('*').remove()\n\n\t\tconst modeRow = colorLegendDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('gap', '10px')\n\t\t\t.style('margin-bottom', '6px')\n\t\t\t.style('flex-wrap', 'wrap')\n\n\t\tmodeRow.append('span').text('Color by')\n\n\t\tconst modes: Array<{ key: 'assayType' | 'cohort' | 'proteinAccession'; label: string }> = [\n\t\t\t{ key: 'assayType', label: 'Assay' },\n\t\t\t{ key: 'cohort', label: 'Cohort' },\n\t\t\t{ key: 'proteinAccession', label: 'Isoform' }\n\t\t]\n\n\t\tfor (const { key, label } of modes) {\n\t\t\tmodeRow\n\t\t\t\t.append('span')\n\t\t\t\t.text(label)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('font-weight', key === colorMode ? '600' : '400')\n\t\t\t\t.style('text-decoration', key === colorMode ? 'underline' : 'none')\n\t\t\t\t.style('color', key === colorMode ? '#111' : '#6b7280')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tcolorMode = key\n\t\t\t\t\tcohortDots.attr('fill', (d: any) => getColor(d)).attr('stroke', (d: any) => getColor(d))\n\t\t\t\t\trenderColorLegend()\n\t\t\t\t})\n\t\t}\n\n\t\tconst makeLegendItems = (items: string[], colorMap: Map<string, string>) => {\n\t\t\tfor (const name of items) {\n\t\t\t\tconst row = colorLegendDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'flex')\n\t\t\t\t\t.style('align-items', 'center')\n\t\t\t\t\t.style('gap', '6px')\n\t\t\t\t\t.style('margin-bottom', '3px')\n\t\t\t\tconst swatch = row\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('width', '10px')\n\t\t\t\t\t.style('height', '10px')\n\t\t\t\t\t.style('border-radius', '50%')\n\t\t\t\t\t.style('background', colorMap.get(name) ?? '#888')\n\t\t\t\t\t.style('opacity', 0.8)\n\t\t\t\t\t.style('flex-shrink', '0')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\tswatch.on('click', (event: any) => {\n\t\t\t\t\tconst menu = new Menu({ padding: '0px' })\n\t\t\t\t\tconst div = menu.d.append('div')\n\t\t\t\t\tconst input: any = div\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t\t\t.style('padding', '0px 10px')\n\t\t\t\t\t\t.text('Color:')\n\t\t\t\t\t\t.append('input')\n\t\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t\t.attr('value', colorMap.get(name) ?? '#888')\n\t\t\t\t\t\t.on('change', () => {\n\t\t\t\t\t\t\tconst newColor = input.node().value\n\t\t\t\t\t\t\tcolorMap.set(name, newColor)\n\t\t\t\t\t\t\tswatch.style('background', newColor)\n\t\t\t\t\t\t\tcohortDots.attr('fill', (d: any) => getColor(d)).attr('stroke', (d: any) => getColor(d))\n\t\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\t})\n\t\t\t\t\tmenu.showunder(event.target)\n\t\t\t\t})\n\t\t\t\trow.append('span').text(name)\n\t\t\t}\n\t\t}\n\n\t\tif (colorMode === 'assayType') {\n\t\t\tmakeLegendItems(assayNames, assayColors)\n\t\t} else if (colorMode === 'cohort') {\n\t\t\tmakeLegendItems(cohortNames, cohortColors)\n\t\t} else if (colorMode === 'proteinAccession') {\n\t\t\tmakeLegendItems(proteinAccessions, proteinColors)\n\t\t}\n\t}\n\n\trenderColorLegend()\n\n\tconst sizeLegendRow = legend\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'flex-start')\n\t\t.style('gap', '8px')\n\t\t.style('margin-top', '8px')\n\n\tsizeLegendRow.append('span').style('display', 'inline-block').style('margin-top', '42px').text('Tested sample size')\n\n\tconst legendSvg = sizeLegendRow.append('svg').attr('width', 190).attr('height', 110).style('display', 'block')\n\n\tnew LegendCircleReference({\n\t\tg: legendSvg.append('g').attr('transform', 'translate(12, 8)'),\n\t\tinputMax: 12,\n\t\tinputMin: 4,\n\t\tmaxLabel: maxTestedN || minTestedN,\n\t\tmaxRadius: radiusScale(Math.max(minTestedN + 1, maxTestedN || minTestedN)),\n\t\tminLabel: minTestedN,\n\t\tminRadius: radiusScale(minTestedN),\n\t\ttitle: '',\n\t\tmenu: {\n\t\t\tminMaxLabel: 'pixels',\n\t\t\tcallback: async () => {}\n\t\t}\n\t})\n}\n\n/*\nfunction renderFCSummary(holder: any, data: any, self: ProteinView) {\n\tholder.selectAll('*').remove()\n\n\t// data.nonPTMAssays store the fold change for each nonPTM assay type, data.PTMs store the PTM data (including fold change) for each PTM assay type\n\tconst nonPTMAssays = data?.nonPTMAssays || []\n\n\tlet maxAbs = 0\n\tfor (const assay of nonPTMAssays) {\n\t\tfor (const c of assay.nonPTMCohorts || []) {\n\t\t\tconst log2ratio = getLog2Ratio(c.value)\n\t\t\tif (log2ratio !== null) maxAbs = Math.max(maxAbs, Math.abs(log2ratio))\n\t\t}\n\t}\n\tif (maxAbs < 0.05) maxAbs = 0.05 // set a minimum scale for better visualization of small fold changes\n\n\tfor (const assay of nonPTMAssays) {\n\t\tconst assayName = assay.assayName\n\t\tconst section = holder.append('div').style('margin-bottom', '18px')\n\t\tsection.append('div').style('font-weight', 600).style('margin-bottom', '8px').text(`${assayName}`)\n\n\t\tconst header = section\n\t\t\t.append('div')\n\t\t\t.style('display', 'grid')\n\t\t\t.style('grid-template-columns', '220px 30% 100px')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '8px')\n\t\t\t.style('margin', '0 0 6px 0')\n\t\t\t.style('font-size', '.75em')\n\t\t\t.style('font-weight', 600)\n\t\t\t.style('color', '#495057')\n\n\t\theader.append('div').text('Cohort')\n\t\tconst scaleHeader = header.append('div').style('position', 'relative').style('height', '14px')\n\n\t\tscaleHeader.append('div').style('position', 'absolute').style('left', 0).style('top', 0).text((-maxAbs).toFixed(2))\n\n\t\tscaleHeader\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('left', '50%')\n\t\t\t.style('top', 0)\n\t\t\t.style('transform', 'translateX(-50%)')\n\t\t\t.text('0')\n\n\t\tscaleHeader.append('div').style('position', 'absolute').style('right', 0).style('top', 0).text(maxAbs.toFixed(2))\n\n\t\theader.append('div').text('log2 fold change')\n\n\t\tfor (const c of assay.nonPTMCohorts || []) {\n\t\t\tconst cohortName = c.cohortName\n\t\t\tconst log2ratio = getLog2Ratio(c.value)\n\t\t\tconst row = section\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'grid')\n\t\t\t\t.style('grid-template-columns', '220px 30% 100px')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('gap', '8px')\n\t\t\t\t.style('margin', '4px 0')\n\n\t\t\trow.append('div').style('font-size', '.9em').text(cohortName)\n\n\t\t\tconst track = row\n\t\t\t\t.append('div')\n\t\t\t\t.style('height', '14px')\n\t\t\t\t.style('background', '#f1f3f4')\n\t\t\t\t.style('border-radius', '7px')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('overflow', 'hidden')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.attr('title', 'Click to show violin plot')\n\t\t\t\t.on('click', () => launchViolinPlot(self, assayName, cohortName))\n\n\t\t\ttrack\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('left', '50%')\n\t\t\t\t.style('top', 0)\n\t\t\t\t.style('bottom', 0)\n\t\t\t\t.style('width', '1px')\n\t\t\t\t.style('transform', 'translateX(-0.5px)')\n\t\t\t\t.style('background', '#868e96')\n\t\t\t\t.style('opacity', 0.7)\n\n\t\t\tconst value = Number.isFinite(log2ratio) ? log2ratio : 0\n\t\t\tconst ratio = maxAbs > 0 ? Math.abs(value as number) / maxAbs : 0\n\t\t\tconst widthPct = Math.max(0, Math.min(50, ratio * 50))\n\t\t\tif (log2ratio !== null && widthPct > 0) {\n\t\t\t\ttrack\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('position', 'absolute')\n\t\t\t\t\t.style('left', log2ratio >= 0 ? '50%' : `${50 - widthPct}%`)\n\t\t\t\t\t.style('top', 0)\n\t\t\t\t\t.style('bottom', 0)\n\t\t\t\t\t.style('width', `${widthPct}%`)\n\t\t\t\t\t.style('background', log2ratio >= 0 ? '#2b8a3e' : '#c92a2a')\n\t\t\t\t\t.style('opacity', 1)\n\t\t\t}\n\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-family', 'monospace')\n\t\t\t\t.style('font-size', '.85em')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.attr('title', 'Click to show violin plot')\n\t\t\t\t.on('click', () => launchViolinPlot(self, assayName, cohortName))\n\t\t\t\t.text(log2ratio !== null ? log2ratio.toFixed(3) : 'NA')\n\t\t}\n\t}\n}\n*/\n\nfunction launchViolinPlot(self: ProteinView, assayName: string, cohortName: string, isoForm: string) {\n\tconst selectedProtein = self.state.config?.tw?.term\n\tif (!selectedProtein) throw new Error('proteinView: selected protein term is missing')\n\n\tconst action: any = {\n\t\ttype: 'plot_create',\n\t\tconfig: {\n\t\t\tchartType: 'summary'\n\t\t}\n\t}\n\n\taction.config.assayCohortTitle = `${assayName}: ${cohortName}`\n\taction.config.proteomeDetails = { assay: assayName, cohort: cohortName }\n\n\tconst termdbConfig = self.app.vocabApi.termdbConfig\n\tconst cohortSelected = termdbConfig?.queries?.proteome?.assays?.[assayName]?.cohorts?.[cohortName]\n\tif (cohortSelected?.filter) action.config.filter = toTvslstFilter(cohortSelected.filter)\n\n\tconst t = structuredClone(selectedProtein)\n\tt.name = `${t.name}: ${isoForm}`\n\tt.proteomeDetails = { assay: assayName, cohort: cohortName }\n\taction.config.term = { term: t, q: { mode: NumericModes.continuous } }\n\n\tif (cohortSelected?.overlayTerm) {\n\t\taction.config.term2 = { term: structuredClone(cohortSelected.overlayTerm), q: {} }\n\t}\n\n\tself.app.dispatch(action)\n}\n\nasync function renderPTMLollipop(holder: any, data: any, self: ProteinView) {\n\tif (!data?.cohorts?.length) return\n\n\tconst custom_variants: any[] = []\n\tconst mergedMclassOverride: any = {}\n\tconst gmCache = new Map()\n\tfor (const ptm of data.cohorts) {\n\t\tif (!ptm.PTMType) continue // filter out non-PTM cohorts\n\t\t//use default gene model to get coordinates for all PTM sites, which is sufficient for most cases\n\t\t//and avoids the complexity of mapping between different isoforms. TODO:support isoform-specific mapping.\n\t\tconst gm = await getGmForPTM(ptm.geneName, self.app.opts.genome.name, gmCache)\n\t\tif (!gm) continue\n\t\tconst logValue = getLog2Ratio(ptm.foldChange)\n\n\t\tif (ptm.mclassOverride && typeof ptm.mclassOverride == 'object') {\n\t\t\tObject.assign(mergedMclassOverride, ptm.mclassOverride)\n\t\t}\n\n\t\tconst site = parsePTMModSites(ptm.modSites)\n\t\tif (!site) continue\n\t\tconst pos = aa2gmcoord(site, gm)\n\t\tif (!Number.isInteger(pos)) continue\n\t\tconst ptmClass = Object.keys(ptm.mclassOverride || {})[0]\n\t\tcustom_variants.push({\n\t\t\tchr: gm.chr,\n\t\t\tpos,\n\t\t\tmname: `${ptm.modSites}: ${ptm.cohortName}`,\n\t\t\tclass: ptmClass,\n\t\t\tdt: 1,\n\t\t\tlogValue\n\t\t})\n\t}\n\tif (!custom_variants.length) return\n\n\tconst mclassOverride = {\n\t\tclassName: 'PTMs',\n\t\tclasses: mergedMclassOverride\n\t}\n\n\t// apply mclass override to global mclass, which will be used by the mds3 track to display the PTM sites.\n\t// this is necessary because the lollipop plot relies on mclass for variant\n\t// TODO: find a better way (such as defining PTM-specific class keys) to pass mclass override to the track\n\t// without modifying global mclass, which can have unintended side effects on other plots.\n\tfor (const key in mclassOverride.classes) {\n\t\tif (mclass[key]) Object.assign(mclass[key], mclassOverride.classes[key])\n\t}\n\n\t// create mds3 custom track using numeric mode with logValue on y-axis\n\tconst tk = {\n\t\ttype: 'mds3',\n\t\tname: 'PTMs',\n\t\tcustom_variants: custom_variants,\n\t\tskewerModes: [\n\t\t\t{\n\t\t\t\ttype: 'numeric',\n\t\t\t\tbyAttribute: 'logValue',\n\t\t\t\tlabel: 'Log2FC Disease vs Control',\n\t\t\t\tinuse: true,\n\t\t\t\taxisheight: 100\n\t\t\t}\n\t\t],\n\t\tmclassOverride\n\t}\n\n\t// launch block in protein mode with custom track\n\tconst arg = {\n\t\tholder: holder.append('div'),\n\t\tgenome: self.app.opts.genome,\n\t\tnobox: true,\n\t\ttklst: [tk],\n\t\tmclassOverride,\n\t\tdebugmode: self.app.opts.debug,\n\t\tquery: data.cohorts[0].geneName\n\t}\n\n\tconst _ = await import('#src/block.init')\n\tawait _.default(arg)\n}\n\n// return the first valid modification site parsed from the modSites string, which is expected to be in the format like \"S10\", or \"S10,T11\"\n// for now return the first valid site for simplicity. TODO: parse and display multiple sites if available.\nfunction parsePTMModSites(modSites: string) {\n\tif (!modSites) return null\n\tconst regex = /([A-Za-z])(\\d+)/g\n\tlet m\n\twhile ((m = regex.exec(modSites)) !== null) {\n\t\tconst position = Number(m[2])\n\t\tif (!Number.isInteger(position) || position < 1) continue\n\t\treturn position\n\t}\n\treturn null\n}\n\nasync function getGmForPTM(geneName: string, genomeName: string, gmCache: Map<string, any>) {\n\tif (!geneName) return null\n\tif (gmCache.has(geneName)) return gmCache.get(geneName)\n\n\tconst d = await dofetch3('genelookup', {\n\t\tbody: {\n\t\t\tdeep: 1,\n\t\t\tgenome: genomeName,\n\t\t\tinput: geneName\n\t\t}\n\t})\n\n\tif (d.error || !Array.isArray(d.gmlst) || !d.gmlst.length) {\n\t\tgmCache.set(geneName, null)\n\t\treturn null\n\t}\n\n\tconst gm = d.gmlst.find((i: any) => i.isdefault) || d.gmlst[0]\n\tgmCache.set(geneName, gm)\n\treturn gm\n}\n\nfunction getLog2Ratio(foldChange: number) {\n\tif (!Number.isFinite(foldChange) || foldChange <= 0) return null\n\treturn Math.log2(foldChange)\n}\n\nexport async function getPlotConfig(opts: any) {\n\tconst config = structuredClone(defaultConfig)\n\tif (!opts.tw) throw new Error('proteinView requires opts.tw')\n\treturn copyMerge(config, opts)\n}\n\nexport function makeChartBtnMenu(holder: any, chartsInstance: any) {\n\tconst row = holder.append('div').style('padding', '5px')\n\trow.append('span').style('font-weight', 'bold').text('Enter a gene name:')\n\n\tconst geneSearch = addGeneSearchbox({\n\t\trow,\n\t\tgenome: chartsInstance.app.opts.genome,\n\t\ttip: new Menu({ padding: '0px' }),\n\t\tsearchOnly: 'gene',\n\t\tcallback: async () => {\n\t\t\tif (!geneSearch.geneSymbol) throw new Error('A valid gene selection is required')\n\t\t\tchartsInstance.dom.tip.hide()\n\t\t\tchartsInstance.app.dispatch({\n\t\t\t\ttype: 'plot_create',\n\t\t\t\tconfig: {\n\t\t\t\t\tchartType: 'proteinView',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\tgene: geneSearch.geneSymbol,\n\t\t\t\t\t\t\tname: geneSearch.geneSymbol,\n\t\t\t\t\t\t\ttype: TermTypes.PROTEOME_ABUNDANCE\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t})\n}\n\nexport const proteinViewInit = getCompInit(ProteinView)\nexport const componentInit = proteinViewInit\n"],
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+  "names": []
+}

package/dist/proteomeAbundance-DE4NVBCN.js

@@ -0,0 +1,21 @@
+import {
+  makeChartBtnMenu,
+  renderAssayAndCohortRadios,
+  toTvslstFilter
+} from "./chunk-HWHG63LH.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  makeChartBtnMenu,
+  renderAssayAndCohortRadios,
+  toTvslstFilter
+};
+//# sourceMappingURL=proteomeAbundance-DE4NVBCN.js.map

package/dist/proteomeAbundance-LTB3QR3G.js

@@ -0,0 +1,63 @@
+import {
+  renderAssayAndCohortRadios
+} from "./chunk-HWHG63LH.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// termdb/handlers/proteomeAbundance.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.opts = opts;
+    this.dom = {};
+    opts.holder.style("padding", "5px 10px 10px 25px");
+    this.assays = this.opts.app.vocabApi.termdbConfig?.queries?.proteome?.assays || {};
+    const assayKeys = Object.keys(this.assays);
+    if (!assayKeys.length) throw "No proteome assays available";
+    const initialProteomeDetails = opts.usecase?.proteomeDetails || {};
+    const selectedAssay = initialProteomeDetails.assay && this.assays[initialProteomeDetails.assay] ? initialProteomeDetails.assay : assayKeys[0];
+    const cohortKeys = Object.keys(this.assays[selectedAssay]?.cohorts || {});
+    if (!cohortKeys.length) throw "No cohorts available for selected assay";
+    const selectedCohort = initialProteomeDetails.cohort && this.assays[selectedAssay]?.cohorts?.[initialProteomeDetails.cohort] ? initialProteomeDetails.cohort : cohortKeys[0];
+    this.proteomeDetails = { assay: selectedAssay, cohort: selectedCohort };
+    this.dom.typeSettingDiv = opts.holder.append("div");
+    renderAssayAndCohortRadios({
+      holder: this.dom.typeSettingDiv,
+      assays: this.assays,
+      selectedProteomeDetails: this.proteomeDetails,
+      onChange: (proteomeDetails) => {
+        const { assay, cohort } = proteomeDetails;
+        this.proteomeDetails = { assay, cohort };
+        void this.updateUsecase();
+      }
+    });
+    await this.updateUsecase();
+  }
+  async updateUsecase() {
+    const { assay, cohort } = this.proteomeDetails;
+    const state = this.opts.app.getState();
+    await this.opts.app.dispatch({
+      type: "app_refresh",
+      state: {
+        tree: {
+          ...state.tree,
+          usecase: {
+            ...state.tree.usecase,
+            proteomeDetails: { assay, cohort }
+          }
+        }
+      }
+    });
+  }
+};
+export {
+  SearchHandler
+};
+//# sourceMappingURL=proteomeAbundance-LTB3QR3G.js.map

package/dist/qualitative-YOFAROVR.js

@@ -0,0 +1,41 @@
+import {
+  QualCustomGS,
+  QualPredefinedGS,
+  QualValues,
+  QualitativeBase
+} from "./chunk-NVB7MQLH.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-4JON7TLI.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  QualCustomGS,
+  QualPredefinedGS,
+  QualValues,
+  QualitativeBase
+};
+//# sourceMappingURL=qualitative-YOFAROVR.js.map