@sjcrh/proteinpaint-client 2.222.0 → 2.223.0

package/dist/chunk-SKL52OWF.js

@@ -1,466 +0,0 @@
-import {
-  mayRunSnplstTask
-} from "./chunk-7OYOC7XY.js";
-import {
-  escapeHtml
-} from "./chunk-4ASBDE27.js";
-
-// termsetting/handlers/snplst.ts
-function getHandler(self) {
-  return {
-    getPillName() {
-      return escapeHtml(self.term.name);
-    },
-    getPillStatus() {
-      if (!self.term?.snps) return;
-      const invalid = self.term.snps.reduce((i, j) => i + (j.invalid || !j.alleles ? 1 : 0), 0);
-      if (invalid) return { text: invalid + " invalid" };
-    },
-    validateQ(data) {
-      validateQ(data);
-    },
-    async showEditMenu(div) {
-      await makeEditMenu(self, div);
-    }
-  };
-}
-async function makeEditMenu(self, div0) {
-  const div = div0.append("div").style("margin", "15px");
-  const select_ancestry = await mayRestrictAncestry(self, div);
-  const inputUIholder = div.append("div");
-  const textarea = inputUIholder.append("textarea").attr("rows", 5).attr("cols", 20).attr("placeholder", "Enter variants");
-  const prompt = inputUIholder.append("div").style("opacity", 0.8).style("font-size", ".8em");
-  prompt.append("div").html(
-    `Enter a list of variants (dbSNP accessions). One variant per line. Max 500 allowed.${self.usecase.target == "dataDownload" ? "" : "<br>Effect alleles (alleles tested against in the analysis) can be specified here or<br>after variant validation."}`
-  );
-  const exampleInput = [
-    { id: "rs1641548", effectAllele: "T" },
-    { id: "rs4968204", effectAllele: "C" },
-    { id: "rs9893249", effectAllele: "T" },
-    { id: "rs1042522", effectAllele: "G" }
-  ];
-  const example1 = prompt.append("ul").style("display", "inline-block").style("list-style-type", "none").style("padding", "0px");
-  const example2 = prompt.append("ul").style("display", self.usecase.target == "dataDownload" ? "none" : "inline-block").style("list-style-type", "none").style("padding", "0px").style("margin-left", "40px");
-  example1.append("li").style("text-decoration", "underline").text("Example:");
-  example2.append("li").style("text-decoration", "underline").text("Example (with effect alleles):");
-  for (const variant of exampleInput) {
-    example1.append("li").text(variant.id);
-    example2.append("li").html(`${variant.id}&nbsp;${variant.effectAllele}`);
-  }
-  const validateBtn = inputUIholder.append("div").style("margin-top", "15px").append("button").text("Validate variants").on("click", async () => {
-    const snps = parseSnpFromText(textarea);
-    if (!snps.length) return window.alert("No valid variants");
-    if (!self.term) {
-      self.term = { id: makeId(), type: "snplst" };
-    }
-    if (self.term.snps) {
-      for (const n of snps) {
-        if (self.term.snps.find((i) => i.rsid == n.rsid)) continue;
-        self.term.snps.push(n);
-      }
-    } else {
-      self.term.snps = snps;
-    }
-    self.term.name = getTermName(self.term.snps);
-    if (!self.q) self.q = {};
-    self.doNotHideTipInMain = true;
-    if (self.dom.pill_termname) {
-      self.dom.pill_termname.text(self.term.name);
-    }
-    validateBtn.text("Validating...").property("disabled", true);
-    try {
-      await validateInput(self);
-    } catch (e) {
-      alert("Error: " + (e.message || e));
-      validateBtn.text("Validate variants").property("disabled", false);
-      return;
-    }
-    if (!Number.isFinite(self.q.AFcutoff)) {
-      self.q.AFcutoff = 5;
-      input_AFcutoff.property("value", self.q.AFcutoff);
-    }
-    if (!Number.isInteger(self.q.alleleType)) {
-      self.q.alleleType = snps.find((snp) => snp.effectAllele) ? 2 : 0;
-      select_alleleType.property("selectedIndex", self.q.alleleType);
-      div.select(".sjpp-allele-type-hint").text(getAlleleTypeHint(select_alleleType));
-    }
-    if (!Number.isInteger(self.q.geneticModel)) {
-      self.q.geneticModel = 0;
-      select_geneticModel.property("selectedIndex", self.q.geneticModel);
-    }
-    if (!Number.isInteger(self.q.missingGenotype)) {
-      self.q.missingGenotype = 0;
-      select_missingGenotype.property("selectedIndex", self.q.missingGenotype);
-    }
-    if (select_ancestry) {
-      self.q.restrictAncestry = select_ancestry.node().options[select_ancestry.property("selectedIndex")].__ancestry_obj;
-    }
-    await makeSampleSummary(self);
-    inputUIholder.style("display", "none");
-    editUIholder.style("display", "");
-    if (self.dom.snplst_table) {
-      renderSnpEditTable(self, select_alleleType);
-    } else {
-      initSnpEditTable(snplstTableDiv, self, select_alleleType);
-    }
-  });
-  const editUIholder = div.append("div");
-  editUIholder.append("p").append("span").html("&laquo; Back to input").attr("class", "sja_clbtext").on("click", () => {
-    inputUIholder.style("display", "");
-    editUIholder.style("display", "none");
-    validateBtn.text("Validate variants").property("disabled", false);
-  });
-  const snplstTableDiv = editUIholder.append("div").style("margin-bottom", "25px");
-  const [input_AFcutoff, select_alleleType, select_geneticModel, select_missingGenotype] = makeSnpSelect(
-    editUIholder.append("div").attr("class", "sjpp-snp-select"),
-    self,
-    "snplst"
-  );
-  if (self.usecase.target == "dataDownload") editUIholder.select(".sjpp-snp-select").style("display", "none");
-  const btnRow = editUIholder.append("div").style("margin-top", "20px");
-  btnRow.append("button").text("Submit").on("click", async () => {
-    self.term.snps = self.term.snps.filter((i) => !i.tobe_deleted);
-    if (self.term.snps.find((snp) => !snp.effectAllele))
-      return window.alert("Effect allele not specified for one or more variants");
-    self.term.name = getTermName(self.term.snps);
-    if (self.dom.pill_termname) {
-      self.dom.pill_termname.text(self.term.name);
-    }
-    try {
-      await validateInput(self);
-    } catch (e) {
-      alert("Error: " + (e.message || e));
-    }
-    {
-      const v = Number(input_AFcutoff.property("value"));
-      self.q.AFcutoff = v < 0 || v >= 100 ? 5 : v;
-    }
-    self.q.alleleType = select_alleleType.property("selectedIndex");
-    self.q.geneticModel = select_geneticModel.property("selectedIndex");
-    self.q.missingGenotype = select_missingGenotype.property("selectedIndex");
-    if (select_ancestry) {
-      self.q.restrictAncestry = select_ancestry.node().options[select_ancestry.property("selectedIndex")].__ancestry_obj;
-    }
-    await makeSampleSummary(self);
-    if (self.dom.snplst_table) {
-      renderSnpEditTable(self, select_alleleType);
-    } else {
-      initSnpEditTable(snplstTableDiv, self, select_alleleType);
-    }
-    delete self.doNotHideTipInMain;
-    self.api.runCallback();
-    self.view.updateUI();
-  });
-  btnRow.append("span").style("padding-left", "15px").style("opacity", 0.8).style("font-size", ".8em").text(
-    self.usecase.target == "dataDownload" ? "" : "Variants will be treated as separate covariates in the regression model"
-  );
-  if (self.term?.snps?.length) {
-    initSnpEditTable(snplstTableDiv, self, select_alleleType);
-    inputUIholder.style("display", "none");
-  } else {
-    editUIholder.style("display", "none");
-  }
-}
-function initSnpEditTable(div, self, select_alleleType) {
-  self.dom.snplst_table = div.append("table");
-  renderSnpEditTable(self, select_alleleType);
-  div.append("p").style("opacity", 0.8).style("font-size", ".8em").style("display", self.usecase.target == "dataDownload" ? "none" : "block").html("Effect alleles are highlighted in red. Click on an allele to set as the effect allele.");
-}
-function renderSnpEditTable(self, select_alleleType) {
-  self.dom.snplst_table.selectAll("*").remove();
-  const title_tr = self.dom.snplst_table.append("tr").style("opacity", 0.4);
-  const col_titles = [
-    { title: "Variants" },
-    { title: "# genotyped<br>samples" },
-    { title: "Reference allele<br>(frequency)" },
-    { title: "Alternative allele(s)<br>(frequency)" },
-    { title: "Genotype<br>(frequency)" },
-    { title: "Delete" }
-  ];
-  if (self.usecase.target == "dataDownload") col_titles.splice(4, 1);
-  col_titles.forEach((c) => {
-    title_tr.append("td").html(c.title).style("font-size", ".8em").style("text-align", "center").style("padding", "8px");
-  });
-  if (!self.term.snps) throw `Missing term.snps [snplst.ts renderSnpEditTable()]`;
-  for (const [i, snp] of self.term.snps.entries()) {
-    let invalid_snp = false;
-    if (snp.invalid || !snp.alleles && !snp.gt2count) invalid_snp = "NOT ANNNOTATED IN COHORT";
-    const rowcolor = (i + 2) % 2 ? "#eee" : "#fff";
-    const tr = self.dom.snplst_table.append("tr").style("background", rowcolor);
-    tr.append("td").text(snp.rsid).style("padding", "8px");
-    const sample_count = invalid_snp ? invalid_snp : snp.gt2count ? Object.values(snp.gt2count).reduce((a, b) => a + b, 0) : `Missing sample count for snp`;
-    tr.append("td").style("text-align", "center").text(sample_count);
-    const ref_allele_td = tr.append("td");
-    const alt_allele_td = tr.append("td");
-    if (!invalid_snp) {
-      if (!snp.alleles) throw `Missing alleles for snp = ${snp} [snplst.ts renderSnpEditTable()]`;
-      const effectAllele = self.q.snp2effAle ? self.q.snp2effAle[snp.rsid] : void 0;
-      const refAllele = snp.alleles.find((s) => s.isRef);
-      const altAlleles = snp.alleles.filter((s) => !s.isRef);
-      if (self.usecase.target == "dataDownload") {
-        const allele_freq = (refAllele.count * 100 / (sample_count * 2)).toFixed(2);
-        const refAlleleText = `${refAllele.allele} (${allele_freq}%)`;
-        ref_allele_td.style("text-align", "center").style("padding", "8px").text(refAlleleText);
-        const altAllelesText = altAlleles.map((al) => {
-          const allele_freq2 = (al.count * 100 / (sample_count * 2)).toFixed(2);
-          return `${al.allele} (${allele_freq2}%)`;
-        }).join(", ");
-        alt_allele_td.style("text-align", "center").style("padding", "8px").text(altAllelesText);
-      } else {
-        createAlleleBtn(refAllele, ref_allele_td, effectAllele, sample_count, snp, rowcolor, tr);
-        for (const al of altAlleles.values()) {
-          createAlleleBtn(al, alt_allele_td, effectAllele, sample_count, snp, rowcolor, tr);
-        }
-      }
-    }
-    if (self.usecase.target != "dataDownload") {
-      const gt_td = tr.append("td");
-      if (!invalid_snp) {
-        const refGT = self.q.snp2refGrp ? self.q.snp2refGrp[snp.rsid] : void 0;
-        if (!snp.gt2count) throw `Missing gt2count for snp = ${snp} [snplst.ts renderSnpEditTable()]`;
-        for (const [gt, freq] of Object.entries(snp.gt2count)) {
-          const gt_freq = (freq * 100 / sample_count).toFixed(2);
-          const gt_div = gt_td.append("div").style("display", "inline-block").style("border", gt == refGT ? "3px solid #ff0000" : `3px solid ${rowcolor}`);
-          gt_div.append("div").style("display", "inline-block").style("padding", "3px 5px").text(`${gt}`);
-          gt_div.append("div").style("display", "inline-block").style("padding", "0px 6px 0px 2px").style("font-size", ".8em").text(`(${gt_freq}%)`);
-        }
-      }
-    }
-    const snp_checkbox = tr.append("td").style("text-align", "center").append("input").attr("type", "checkbox").on("change", () => {
-      snp.tobe_deleted = snp_checkbox.node().checked;
-    });
-  }
-  function createAlleleBtn(al, td, effectAllele, sample_count, snp, rowcolor, tr) {
-    const allele_freq = (al.count * 100 / (sample_count * 2)).toFixed(2);
-    const allele_div = td.style("text-align", "center").append("button").style("display", "inline-block").style("margin", "0px 3px").style("padding", "3px 7px").style("border-radius", "3px").style("background-color", "#d9ead3").style("border", al.allele == effectAllele ? "3px solid #ff0000" : `3px solid ${rowcolor}`).on("mouseover", () => {
-      if (snp.effectAllele && snp.effectAllele == al.allele) return;
-      else {
-        allele_div.style("background-color", "#fff2cc").style("cursor", "pointer");
-      }
-    }).on("mouseout", () => {
-      if (snp.effectAllele && snp.effectAllele == al.allele) return;
-      else {
-        allele_div.style("background", "#d9ead3");
-      }
-    }).on("click", () => {
-      snp.effectAllele = al.allele;
-      tr.selectAll("button").style("border", "none");
-      allele_div.style("border", "3px solid #ff0000").style("background", "#d9ead3");
-      select_alleleType.selectAll("option").nodes()[2].selected = "selected";
-    });
-    allele_div.append("div").style("display", "inline-block").text(`${al.allele}  `);
-    allele_div.append("div").style("display", "inline-block").style("margin", "0px 5px").style("font-size", ".8em").text(`(${allele_freq}%)`);
-  }
-}
-function getTermName(snps) {
-  if (snps.length == 1) {
-    const s = snps[0];
-    if (s.rsid) return s.rsid;
-    return s.chr + ":" + s.pos;
-  }
-  return snps.length + " variant" + (snps.length > 1 ? "s" : "");
-}
-function parseSnpFromText(textarea) {
-  const text = textarea.property("value");
-  const snps = [];
-  for (const tmp of text.trim().split("\n")) {
-    const [rsid, ale] = tmp.trim().split(/[\s\t]/);
-    if (!rsid) continue;
-    if (snps.find((i) => i.rsid == rsid)) continue;
-    const s = { rsid };
-    if (ale) s.effectAllele = ale;
-    snps.push(s);
-  }
-  if (snps.length > 500) return snps.slice(0, 500);
-  return snps;
-}
-function snp2text(self) {
-  if (!self.term || !self.term.snps) return "";
-  const lines = [];
-  for (const a of self.term.snps) {
-    const l = a.rsid + (a.effectAllele ? " " + a.effectAllele : "");
-    lines.push(l);
-  }
-  return lines.join("\n");
-}
-async function validateInput(self) {
-  const data = await self.vocabApi.validateSnps({ text: snp2text(self) });
-  if (data.error) throw data.error;
-  self.q.cacheid = data.cacheid;
-  if (!self.term.snps) throw `Missing term.snps [snplst.ts validateInput()]`;
-  for (const [i, s] of self.term.snps.entries()) {
-    const s1 = data.snps[i];
-    s.snpid = s1.snpid;
-    s.invalid = s1.invalid;
-  }
-}
-async function makeSampleSummary(self) {
-  const body = { cacheid: self.q.cacheid };
-  const extraFilters = [];
-  let f;
-  if (self.q.restrictAncestry) {
-    if (self.filter) {
-      f = structuredClone(self.filter);
-      const idx = f.lst.findIndex((i) => i.tvs?.term?.id == self.q.restrictAncestry.tvs.term.id);
-      if (idx != -1) {
-        f.lst[idx] = { type: "tvs", tvs: self.q.restrictAncestry.tvs };
-      } else {
-        extraFilters.push({ type: "tvs", tvs: self.q.restrictAncestry.tvs });
-      }
-    } else {
-      extraFilters.push({ type: "tvs", tvs: self.q.restrictAncestry.tvs });
-    }
-  } else {
-    if (self.filter) extraFilters.push(self.filter);
-  }
-  const filter = { type: "tvslst", join: "and", lst: [...extraFilters] };
-  if (f) filter.lst.push(f);
-  const data = await self.vocabApi.getCategories(self.term, filter, body);
-  mayRunSnplstTask(
-    {
-      term: self.term,
-      q: self.q
-    },
-    //quick fix for $id being required in BaseTw type
-    data
-  );
-}
-function validateQ(data) {
-  if (!Number.isFinite(data.q.AFcutoff)) throw "AFcutoff is not number";
-  if (data.q.AFcutoff < 0 || data.q.AFcutoff > 100) throw "AFcutoff is not within 0 to 100";
-  if (![0, 1, 2].includes(data.q.alleleType)) throw "alleleType value is not one of 0/1";
-  if (![0, 1, 2, 3].includes(data.q.geneticModel)) throw "geneticModel value is not one of 0/1";
-  if (![0, 1].includes(data.q.missingGenotype)) throw "missingGenotype value is not one of 0/1";
-}
-async function fillTW(tw, vocabApi) {
-  try {
-    validateQ(tw);
-  } catch (e) {
-    throw "snplst validateQ(): " + e;
-  }
-  if (!Array.isArray(tw.term.snps)) throw "tw.term.snps[] is not an array";
-  if (tw.term.snps.length == 0) throw "tw.term.snps[] array is 0 length";
-  if (!tw.term.name) tw.term.name = getTermName(tw.term.snps);
-  if (tw.id == void 0 || tw.id == "") {
-    if (tw.term.id == void 0 || tw.term.id == "") {
-      tw.term.id = makeId();
-    }
-    tw.id = tw.term.id;
-  } else {
-    if (tw.term.id == void 0 || tw.term.id == "") {
-      tw.term.id = tw.id;
-    }
-  }
-  await validateInput({
-    term: tw.term,
-    q: tw.q,
-    vocabApi
-  });
-}
-function makeId() {
-  return "snplst" + Math.random();
-}
-function makeSnpSelect(div, self, termtype) {
-  let input_AFcutoff_label, input_AFcutoff, select_missingGenotype;
-  {
-    input_AFcutoff_label = div.append("div").style("opacity", 0.5).style("font-size", ".8em").style("margin-bottom", "2px").text("EFFECT ALLELE FREQUENCY CUTOFF");
-    self.dom.input_AFcutoff_label = input_AFcutoff_label;
-    const row = div.append("div");
-    input_AFcutoff = row.append("input").attr("type", "number").attr("min", 0).attr("max", 100).property("value", 5).style("border-color", "#858585").style("margin", "0px");
-    row.append("span").text("%");
-    let text;
-    if (termtype == "snplst") {
-      text = "Variants below this cutoff are discarded";
-    } else {
-      if (self.usecase.regressionType == "linear") {
-        text = "Variants below this cutoff are analyzed by the Wilcoxon rank sum test";
-      } else if (self.usecase.regressionType == "logistic") {
-        text = "Variants below this cutoff are analyzed by the Fisher's exact test";
-      } else {
-        text = "Variants below this cutoff are analyzed by the cumulative incidence test";
-      }
-    }
-    row.append("span").style("margin-left", "10px").style("opacity", 0.5).style("font-size", ".7em").style("font-style", "italic").text(text);
-  }
-  div.append("div").style("margin-top", "15px").style("opacity", 0.5).style("font-size", ".8em").style("margin-bottom", "2px").text("SET EFFECT ALLELE AS");
-  const select_alleleType = div.append("select");
-  select_alleleType.append("option").text("Minor allele");
-  select_alleleType.append("option").text("Alternative allele");
-  if (termtype !== "snplocus") {
-    select_alleleType.append("option").text("Custom allele");
-  }
-  div.append("div").attr("class", "sjpp-allele-type-hint").style("display", "inline-block").style("margin-left", "15px").style("opacity", 0.5).style("font-size", ".7em").style("font-style", "italic").text(getAlleleTypeHint(select_alleleType));
-  select_alleleType.on("change", async () => {
-    div.select(".sjpp-allele-type-hint").text(getAlleleTypeHint(select_alleleType));
-    self.q.alleleType = select_alleleType.property("selectedIndex");
-    if (termtype !== "snplocus") {
-      if (!self.term.snps) throw `Missing term.snps [snplst.ts makeSnpSelect()]`;
-      for (const snp of self.term.snps) {
-        snp.effectAllele = false;
-      }
-      await makeSampleSummary(self);
-      renderSnpEditTable(self, select_alleleType);
-    }
-  });
-  div.append("div").style("margin-top", "15px").style("margin-bottom", "2px").style("opacity", 0.5).style("font-size", ".8em").text("GENETIC MODEL");
-  const select_geneticModel = div.append("select");
-  select_geneticModel.append("option").text("Additive: EE=2, EN=1, NN=0");
-  select_geneticModel.append("option").text("Dominant: EE=1, EN=1, NN=0");
-  select_geneticModel.append("option").text("Recessive: EE=1, EN=0, NN=0");
-  select_geneticModel.append("option").text("By genotype: EE and EN compared to NN");
-  div.append("div").style("display", "inline-block").style("margin-left", "15px").style("opacity", 0.5).style("font-size", ".7em").style("font-style", "italic").html("E = effect allele; N = non-effect allele");
-  const missingGenotypeLabel = div.append("div").style("margin-top", "15px").style("opacity", 0.5).style("font-size", ".7em");
-  if (termtype == "snplocus") {
-    missingGenotypeLabel.text("Samples with missing genotypes are dropped.");
-  } else {
-    missingGenotypeLabel.text("MISSING GENOTYPE").style("font-size", ".8em").style("margin-bottom", "2px");
-    select_missingGenotype = div.append("select");
-    select_missingGenotype.append("option").text("Impute as homozygous for non-effect allele");
-    select_missingGenotype.append("option").text("Drop sample");
-  }
-  if (Number.isInteger(self.q?.alleleType)) select_alleleType.property("selectedIndex", self.q.alleleType);
-  if (Number.isFinite(self.q?.AFcutoff)) input_AFcutoff.property("value", self.q.AFcutoff);
-  if (Number.isInteger(self.q?.geneticModel)) select_geneticModel.property("selectedIndex", self.q.geneticModel);
-  if (select_missingGenotype && Number.isInteger(self.q?.missingGenotype))
-    select_missingGenotype.property("selectedIndex", self.q.missingGenotype);
-  return [input_AFcutoff, select_alleleType, select_geneticModel, select_missingGenotype];
-}
-async function mayRestrictAncestry(self, holder) {
-  if (self.q?.doNotRestrictAncestry) return;
-  const tdbcfg = await self.vocabApi.getTermdbConfig();
-  if (!tdbcfg.restrictAncestries) return;
-  const row = holder.append("div").style("margin-bottom", "15px");
-  self.dom.restrictAncestriesRow = row;
-  row.append("span").text("Restrict analysis to").style("margin-right", "5px").style("opacity", 0.5);
-  const select = row.append("select");
-  for (const ancestry of tdbcfg.restrictAncestries) {
-    const opt = select.append("option").text(ancestry.name);
-    opt.node().__ancestry_obj = ancestry;
-  }
-  if (self.q && self.q.restrictAncestry) {
-    const i = tdbcfg.restrictAncestries.findIndex((i2) => i2.name == self.q.restrictAncestry.name);
-    if (i == -1) throw "unknown restrictAncestry: " + self.q.restrictAncestry.name;
-    select.property("selectedIndex", i);
-  }
-  return select;
-}
-function getAlleleTypeHint(select_alleleType) {
-  let hint;
-  const i = select_alleleType.property("selectedIndex");
-  if (i == 0) {
-    hint = "For multi-allelic variants, the second most common allele is used as the effect allele";
-  } else if (i == 1) {
-    hint = "For multi-allelic variants, the most common alternative allele is used as the effect allele";
-  } else {
-    hint = "";
-  }
-  return hint;
-}
-
-export {
-  getHandler,
-  fillTW,
-  makeSnpSelect,
-  mayRestrictAncestry
-};
-//# sourceMappingURL=chunk-SKL52OWF.js.map

package/dist/chunk-TRWUXFVB.js

@@ -1,102 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-VZ2JWFSX.js";
-import {
-  fillTermWrapper
-} from "./chunk-4ASBDE27.js";
-import {
-  dictionaryNumericTypes,
-  numericTypes
-} from "./chunk-JHLF2ZC2.js";
-import {
-  copyMerge
-} from "./chunk-HBNB5TRH.js";
-
-// plots/matrix/hierCluster.config.js
-async function getPlotConfig2(opts = {}, app) {
-  opts.chartType = "hierCluster";
-  if (dictionaryNumericTypes.has(opts.dataType) || opts.dataType == "numericDictTerm") {
-    const grp = opts.termgroups?.find((g) => g.type == "hierCluster");
-    for (const tw of grp?.lst || []) tw.q = { ...tw.q, mode: "continuous" };
-  }
-  const config = await getPlotConfig(opts, app);
-  delete config.genes;
-  if (config.dataType == "numericDictTerm") {
-    const lst = config.termgroups?.find((g) => g.type == "hierCluster")?.lst;
-    config.dataType = lst?.[0]?.term?.type || "float";
-  }
-  config.settings.hierCluster = {
-    /* type of data used for clustering
-    exciting todo: (to introduce new dt values)
-    - gene dependency
-    - numeric dic term
-    - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
-    - metabolite
-    */
-    dataType: config.dataType,
-    // adjust the default group name based on automatically detected term types
-    // Done in matrix.cells.js: setHierClusterCellProps
-    // termGroupName: 'Expression',
-    clusterSamples: true,
-    clusterRows: true,
-    clusterMethod: "average",
-    // complete
-    distanceMethod: "euclidean",
-    zScoreCap: 5,
-    zScoreTransformation: true,
-    xDendrogramHeight: 100,
-    yDendrogramHeight: 200,
-    colorScale: "blueWhiteRed"
-  };
-  const overrides = app.vocabApi.termdbConfig.hierCluster || {};
-  const numericDictTermClusterOverrides = dictionaryNumericTypes.has(config.dataType) && app.vocabApi.termdbConfig.numericDictTermCluster ? app.vocabApi.termdbConfig.numericDictTermCluster : {};
-  copyMerge(
-    config.settings.hierCluster,
-    overrides.settings,
-    opts.settings?.hierCluster || {},
-    numericDictTermClusterOverrides.settings
-  );
-  {
-    const c = config.settings.hierCluster.colorScale;
-    if (!c) throw "colorScale missing";
-  }
-  config.settings.matrix.collabelpos = "top";
-  const termGroupName = config.settings.hierCluster.termGroupName;
-  const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
-    name: termGroupName
-  };
-  hcTermGroup.type = "hierCluster";
-  if (!hcTermGroup.lst?.length) {
-    if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
-    const promises = [];
-    for (const i of opts.terms) {
-      const tw = i.term ? i : { term: i };
-      if (!tw.term.type) {
-        if (config.dataType && numericTypes.has(config.dataType)) {
-          tw.term.type = config.dataType;
-        } else {
-          throw `term type missing and cannot be assigned by dataType '${config.dataType}'`;
-        }
-      } else if (!numericTypes.has(tw.term.type)) {
-        throw "term type is not numeric";
-      } else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
-        throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
-      }
-      if (dictionaryNumericTypes.has(tw.term.type)) tw.q = { ...tw.q, mode: "continuous" };
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    hcTermGroup.lst = await Promise.all(promises);
-    if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
-  }
-  config.settings.matrix.maxSample = 1e5;
-  return config;
-}
-function canTermBeInHierGrp(grpType, twType) {
-  if (dictionaryNumericTypes.has(grpType) && dictionaryNumericTypes.has(twType)) return true;
-  return twType == grpType;
-}
-
-export {
-  getPlotConfig2 as getPlotConfig
-};
-//# sourceMappingURL=chunk-TRWUXFVB.js.map