@sjcrh/proteinpaint-client 2.203.0 → 2.203.1

package/dist/chunk-J3TIXBCS.js

@@ -1,276 +0,0 @@
-import {
-  parsesample
-} from "./chunk-HENLCRVM.js";
-import {
-  dtfusionrna,
-  dtsv,
-  mclassfusionrna,
-  mclasssv
-} from "./chunk-4QBRVM4V.js";
-
-// ../shared/utils/dist/src/bulk.sv.js
-function parseheader(line, flag, issv) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for fusions";
-  const htry = (...lst) => {
-    for (const a of lst) {
-      const j = header.indexOf(a);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("gene_a", "gene1", "genea");
-  if (i == -1) return "gene_a missing from header";
-  header[i] = "gene1";
-  i = htry("gene_b", "gene2", "geneb");
-  if (i == -1) return "gene_b missing from header";
-  header[i] = "gene2";
-  i = htry("chr_a", "chr1", "chra");
-  if (i == -1) return "chr_a missing from header";
-  header[i] = "chr1";
-  i = htry("chr_b", "chr2", "chrb");
-  if (i == -1) return "chr_b missing from header";
-  header[i] = "chr2";
-  i = htry("pos_a", "position_a", "position1", "posa");
-  if (i == -1) return "pos_a missing from header";
-  header[i] = "position1";
-  i = htry("pos_b", "position_b", "position2", "posb");
-  if (i == -1) return "pos_b missing from header";
-  header[i] = "position2";
-  i = htry("isoform_a", "refseq_a", "refseq1", "isoform1", "sv_refseqa");
-  if (i == -1) return "isoform_a missing from header";
-  header[i] = "isoform1";
-  i = htry("isoform_b", "refseq_b", "refseq2", "isoform2", "sv_refseqb");
-  if (i == -1) return "isoform_b missing from header";
-  header[i] = "isoform2";
-  i = htry("strand_a", "orta");
-  if (i == -1) return "strand_a missing from header";
-  header[i] = "strand1";
-  i = htry("strand_b", "ortb");
-  if (i == -1) return "strand_b missing from header";
-  header[i] = "strand2";
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  i = htry("disease");
-  if (i != -1) header[i] = "disease";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  if (issv) {
-    flag.sv.loaded = true;
-    flag.sv.header = header;
-  } else {
-    flag.fusion.loaded = true;
-    flag.fusion.header = header;
-  }
-  return false;
-}
-function parseline(i, line, flag, issv) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  const header = issv ? flag.sv.header : flag.fusion.header;
-  const badlines = issv ? flag.sv.badlines : flag.fusion.badlines;
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.chr1) {
-    badlines.push([i, "missing chr1", lst]);
-    return;
-  }
-  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
-    m.chr1 = "chr" + m.chr1;
-  }
-  if (!m.chr2) {
-    badlines.push([i, "missing chr2", lst]);
-    return;
-  }
-  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
-    m.chr2 = "chr" + m.chr2;
-  }
-  let v = m.position1;
-  if (!v) {
-    badlines.push([i, "missing position1", lst]);
-    return;
-  }
-  let v2 = Number.parseInt(v);
-  if (Number.isNaN(v2) || v2 <= 0) {
-    badlines.push([i, "invalid value for position1", lst]);
-    return;
-  }
-  m.position1 = v2;
-  v = m.position2;
-  if (!v) {
-    badlines.push([i, "missing position2", lst]);
-    return;
-  }
-  v2 = Number.parseInt(v);
-  if (Number.isNaN(v2) || v2 <= 0) {
-    badlines.push([i, "invalid value for position2", lst]);
-    return;
-  }
-  m.position2 = v2;
-  if (parsesample(m, flag, i, lst)) {
-    return;
-  }
-  if (m.isoform1 && m.isoform1.indexOf(",") != -1) {
-    const lst2 = m.isoform1.split(",");
-    m.isoform1 = void 0;
-    for (const t of lst2) {
-      if (t != "") m.isoform1 = t;
-    }
-  }
-  if (m.isoform2 && m.isoform2.indexOf(",") != -1) {
-    const lst2 = m.isoform2.split(",");
-    m.isoform2 = void 0;
-    for (const t of lst2) {
-      if (t != "") m.isoform2 = t;
-    }
-  }
-  if (!m.gene1) {
-    m.isoform1 = void 0;
-  }
-  if (!m.gene2) {
-    m.isoform2 = void 0;
-  }
-  if (m.gene1) {
-    flag.good++;
-    const m2 = {
-      dt: issv ? dtsv : dtfusionrna,
-      class: issv ? mclasssv : mclassfusionrna,
-      isoform: m.isoform1,
-      mname: m.gene2 || m.chr2,
-      sample: m.sample,
-      patient: m.patient,
-      sampletype: m.sampletype,
-      origin: m.origin,
-      disease: m.disease,
-      pairlst: [
-        {
-          a: {
-            name: m.gene1,
-            isoform: m.isoform1,
-            strand: m.strand1,
-            chr: m.chr1,
-            position: m.position1
-          },
-          b: {
-            name: m.gene2,
-            isoform: m.isoform2,
-            strand: m.strand2,
-            chr: m.chr2,
-            position: m.position2
-          }
-        }
-      ]
-    };
-    const n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1;
-    if (!flag.data[n]) {
-      flag.data[n] = [];
-    }
-    flag.data[n].push(m2);
-  }
-  if (m.gene2 && m.gene2 != m.gene1) {
-    flag.good++;
-    const m2 = {
-      dt: issv ? dtsv : dtfusionrna,
-      class: issv ? mclasssv : mclassfusionrna,
-      isoform: m.isoform2,
-      mname: m.gene1 || m.chr1,
-      sample: m.sample,
-      patient: m.patient,
-      sampletype: m.sampletype,
-      origin: m.origin,
-      disease: m.disease,
-      pairlst: [
-        {
-          a: {
-            name: m.gene1,
-            isoform: m.isoform1,
-            strand: m.strand1,
-            chr: m.chr1,
-            position: m.position1
-          },
-          b: {
-            name: m.gene2,
-            isoform: m.isoform2,
-            strand: m.strand2,
-            chr: m.chr2,
-            position: m.position2
-          }
-        }
-      ]
-    };
-    const n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2;
-    if (!flag.data[n]) {
-      flag.data[n] = [];
-    }
-    flag.data[n].push(m2);
-  }
-}
-function duplicate(m) {
-  const n = {};
-  for (const k in m) {
-    if (k == "pairlst") continue;
-    const v = m[k];
-    const type = typeof v;
-    if (type == "object") {
-      continue;
-    }
-    n[k] = v;
-  }
-  if (m.pairlst) {
-    n.pairlst = [];
-    for (const pair of m.pairlst) {
-      const p = {};
-      for (const k in pair) {
-        if (k == "a" || k == "b" || k == "interstitial") {
-          continue;
-        }
-        p[k] = pair[k];
-      }
-      if (pair.a) {
-        p.a = {};
-        for (const k in pair.a) {
-          const v = pair.a[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.a[k] = v;
-        }
-      }
-      if (pair.b) {
-        p.b = {};
-        for (const k in pair.b) {
-          const v = pair.b[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.b[k] = v;
-        }
-      }
-      if (pair.interstitial) {
-        p.interstitial = {};
-        for (const k in pair.interstitial) {
-          const v = pair.interstitial[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.interstitial[k] = v;
-        }
-      }
-      n.pairlst.push(p);
-    }
-  }
-  return n;
-}
-
-export {
-  parseheader,
-  parseline,
-  duplicate
-};
-//# sourceMappingURL=chunk-J3TIXBCS.js.map

package/dist/chunk-JJHMFHRC.js

@@ -1,257 +0,0 @@
-import {
-  getMclassSorter,
-  getSampleGroupSorter,
-  getSampleSorter,
-  getTermSorter
-} from "./chunk-XPSUKXMF.js";
-import {
-  sample_match_termvaluesetting
-} from "./chunk-4WF3XDQP.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtgeneexpression,
-  dtsnvindel
-} from "./chunk-4QBRVM4V.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/matrix.groups.js
-var matrix_groups_exports = {};
-__export(matrix_groups_exports, {
-  classifyValues: () => classifyValues,
-  getSampleGroups: () => getSampleGroups,
-  getSampleOrder: () => getSampleOrder,
-  getTermOrder: () => getTermOrder,
-  stackSiblingCellsByClass: () => stackSiblingCellsByClass
-});
-function getTermOrder(data) {
-  const s = this.settings.matrix;
-  this.termSorter = getTermSorter(this, s);
-  const termOrder = [];
-  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
-  this.mclassSorter = getMclassSorter(this);
-  for (const [grpIndex, grp] of this.termGroups.entries()) {
-    const lst = [];
-    for (const [index, tw] of grp.lst.entries()) {
-      const counts = { samples: 0, hits: 0 };
-      const countedSamples = /* @__PURE__ */ new Set();
-      for (const sd of data.lst) {
-        if (countedSamples.has(sd.sample)) continue;
-        countedSamples.add(sd.sample);
-        const anno = sd[tw.$id];
-        if (anno) {
-          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
-          anno.filteredValues = filteredValues;
-          anno.countedValues = countedValues;
-          anno.renderedValues = renderedValues;
-          if (anno.countedValues?.length) {
-            const v = tw.term.values?.[anno.value];
-            if (v?.uncountable) continue;
-            counts.samples += 1;
-            counts.hits += anno.countedValues.length;
-            if (tw.q?.mode == "continuous") {
-              const v2 = anno.value;
-              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
-              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
-            }
-          }
-        }
-      }
-      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
-      if (grp.type == "hierCluster") numClusterTerms++;
-    }
-    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
-    const processedLst = lst.filter((t) => {
-      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
-      if (!grp.settings) return true;
-      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
-    }).sort(termSorter);
-    if (!processedLst.length) continue;
-    for (const [index, t] of processedLst.entries()) {
-      const { tw, counts } = t;
-      const ref = data.refs.byTermId[t.tw.$id] || {};
-      termOrder.push({
-        grp,
-        grpIndex,
-        visibleGrpIndex,
-        tw,
-        index,
-        // rendered index
-        lstIndex: t.index,
-        // as-listed index, before applying term filters
-        processedLst,
-        prevGrpTotalIndex: totalIndex,
-        totalIndex: totalIndex + index,
-        ref,
-        allCounts: counts
-        // note: term label will be assigned after sample counts are known
-        // label: t.tw.label || t.tw.term.name,
-      });
-    }
-    totalIndex += processedLst.length;
-    visibleGrpIndex += 1;
-  }
-  this.numTerms = termOrder.length;
-  this.numClusterTerms = numClusterTerms;
-  return termOrder;
-}
-function getSampleGroups(data) {
-  const s = this.settings.matrix;
-  const defaultSampleGrp = {
-    id: this.config.divideBy?.$id,
-    name: this.config.divideBy ? "Not annotated" : "",
-    lst: []
-  };
-  const sampleGroups = /* @__PURE__ */ new Map();
-  const term = this.config.divideBy?.term || {};
-  const $id = this.config.divideBy?.$id || "-";
-  const exclude = this.config.divideBy?.exclude || [];
-  const values = term.values || {};
-  const ref = data.refs.byTermId[$id] || {};
-  for (const row of data.lst) {
-    if ($id in row) {
-      const cell = row[$id];
-      const keys = term.type == "multivalue" && Array.isArray(cell.values) ? cell.values.map((v) => v.key) : [cell.key];
-      for (const key of keys) {
-        const name = key in values && values[key].label ? values[key].label : key;
-        if (!sampleGroups.has(key)) {
-          const grp = {
-            name: `${name}`,
-            // convert to a string
-            id: key,
-            lst: [],
-            tw: this.config.divideBy,
-            legendGroups: {},
-            isExcluded: exclude.includes(key)
-          };
-          if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
-          else delete grp.order;
-          sampleGroups.set(key, grp);
-        }
-        sampleGroups.get(key).lst.push(row);
-      }
-    } else {
-      defaultSampleGrp.lst.push(row);
-    }
-  }
-  const sampleGrpsArr = [...sampleGroups.values()];
-  const n = sampleGroups.size;
-  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
-    const l = s.controlLabels;
-    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
-  }
-  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
-    sampleGroups.set(void 0, defaultSampleGrp);
-    sampleGrpsArr.push(...sampleGroups.values());
-  }
-  this.asListedSampleOrder = [];
-  for (const grp of sampleGrpsArr) {
-    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
-  }
-  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
-  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
-    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
-  });
-  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
-  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
-  const dataFilter = (d) => allowedSamples.includes(d);
-  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
-  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
-  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
-  for (const grp of sampleGrpsArr) {
-    grp.lst = grp.lst.filter(dataFilter);
-    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
-    grp.lst.sort(grpLstSampleSorter);
-  }
-  const sampleGrpSorter = getSampleGroupSorter(this);
-  return sampleGrpsArr.sort(sampleGrpSorter);
-}
-function getSampleOrder(data) {
-  const s = this.settings.matrix;
-  this.visibleSampleGrps = /* @__PURE__ */ new Set();
-  const sampleOrder = [];
-  let total = 0, numHiddenGrps = 0;
-  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
-    if (!grp.lst.length) continue;
-    if (grp.isExcluded) numHiddenGrps++;
-    let processedLst = grp.lst;
-    for (const [index, row] of processedLst.entries()) {
-      sampleOrder.push({
-        grp,
-        grpIndex: grpIndex - numHiddenGrps,
-        // : this.sampleGroups.length,
-        row,
-        index,
-        prevGrpTotalIndex: total,
-        totalIndex: total + index,
-        totalHtAdjustments: 0,
-        // may be required when transposed???
-        grpTotals: { htAdjustment: 0 },
-        // may be required when transposed???
-        processedLst
-      });
-    }
-    if (!grp.isExcluded) total += processedLst.length;
-    this.visibleSampleGrps.add(grp);
-  }
-  this.unfilteredSampleOrder = sampleOrder;
-  return sampleOrder.filter((so) => !so.grp.isExcluded);
-}
-function classifyValues(anno, tw, grp, s, sample) {
-  const values = "value" in anno ? [anno.value] : anno.values;
-  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
-  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
-  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
-    throw `unknown matrix value filter type='${isSpecific.type}'`;
-  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
-  const renderedValues = [];
-  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
-    filteredValues.sort(this.mclassSorter);
-    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
-    else {
-      const sortedFilteredValues = [];
-      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
-        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
-        if (v) renderedValues.push(v);
-        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
-        sortedFilteredValues.push(...oneDtV);
-      }
-      filteredValues = sortedFilteredValues;
-    }
-  } else {
-    renderedValues.push(...filteredValues);
-  }
-  return {
-    filteredValues,
-    countedValues: filteredValues.filter((v) => {
-      if (tw.term.type == "geneVariant") {
-        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
-          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
-          if (!groupset) throw "groupset not found";
-          const group = groupset.groups[0];
-          if (v != group.name) return false;
-        } else {
-          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
-            return false;
-        }
-      }
-      return true;
-    }),
-    renderedValues
-  };
-}
-function stackSiblingCellsByClass(a, b) {
-  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
-}
-
-export {
-  getTermOrder,
-  getSampleGroups,
-  getSampleOrder,
-  classifyValues,
-  stackSiblingCellsByClass,
-  matrix_groups_exports
-};
-//# sourceMappingURL=chunk-JJHMFHRC.js.map

package/dist/chunk-JJHMFHRC.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/matrix/matrix.groups.js"],
-  "sourcesContent": ["import { sample_match_termvaluesetting } from '#shared/filter.js'\nimport { getSampleSorter, getTermSorter, getSampleGroupSorter, getMclassSorter } from './matrix.sort'\nimport { dtsnvindel, dtcnv, dtfusionrna, dtgeneexpression, dtsv } from '#shared/common.js'\n\nexport function getTermOrder(data) {\n\tconst s = this.settings.matrix\n\tthis.termSorter = getTermSorter(this, s)\n\t//this.termGroups = JSON.parse(JSON.stringify(this.config.termgroups))\n\tconst termOrder = []\n\tlet totalIndex = 0,\n\t\tvisibleGrpIndex = 0,\n\t\tnumClusterTerms = 0\n\n\tthis.mclassSorter = getMclassSorter(this)\n\tfor (const [grpIndex, grp] of this.termGroups.entries()) {\n\t\tconst lst = [] // will derive a mutable copy of grp.lst\n\t\tfor (const [index, tw] of grp.lst.entries()) {\n\t\t\tconst counts = { samples: 0, hits: 0 }\n\t\t\tconst countedSamples = new Set()\n\t\t\t// sd = sample data, s = this.settings.matrix\n\t\t\tfor (const sd of data.lst) {\n\t\t\t\tif (countedSamples.has(sd.sample)) continue\n\t\t\t\tcountedSamples.add(sd.sample)\n\t\t\t\tconst anno = sd[tw.$id]\n\t\t\t\tif (anno) {\n\t\t\t\t\t// This is the first time classifyValues(), to help sort\n\t\t\t\t\t// terms by sample counts (to the top) and samples by hits\n\t\t\t\t\t// (if applicable, to the left)\n\t\t\t\t\t//\n\t\t\t\t\t// This call will determine what is considered \"visible\",\n\t\t\t\t\t// even when columns are out-of-view when zoomed-in.\n\t\t\t\t\t//\n\t\t\t\t\t// NOTE: the displayed case counts or variant hits are determined\n\t\t\t\t\t// not in this call, but in the second call to\n\t\t\t\t\t// classifyValues(), + in getSerieses() and getLegendData()\n\t\t\t\t\tconst { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd)\n\t\t\t\t\tanno.filteredValues = filteredValues\n\t\t\t\t\tanno.countedValues = countedValues\n\t\t\t\t\tanno.renderedValues = renderedValues\n\t\t\t\t\tif (anno.countedValues?.length) {\n\t\t\t\t\t\tconst v = tw.term.values?.[anno.value]\n\t\t\t\t\t\tif (v?.uncountable) continue\n\t\t\t\t\t\tcounts.samples += 1\n\t\t\t\t\t\tcounts.hits += anno.countedValues.length\n\t\t\t\t\t\tif (tw.q?.mode == 'continuous') {\n\t\t\t\t\t\t\tconst v = anno.value\n\t\t\t\t\t\t\tif (!('minval' in counts) || counts.minval > v) counts.minval = v\n\t\t\t\t\t\t\tif (!('maxval' in counts) || counts.maxval < v) counts.maxval = v\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\tif (grp.type != 'hierCluster' || counts.samples) lst.push({ tw, counts, index })\n\t\t\tif (grp.type == 'hierCluster') numClusterTerms++\n\t\t}\n\n\t\t// may override the settings.sortTermsBy with a sorter that is specific to a term group\n\t\tconst termSorter = grp.sortTermsBy || grp.type == 'hierCluster' ? getTermSorter(this, s, grp) : this.termSorter\n\t\tconst processedLst = lst\n\t\t\t.filter(t => {\n\t\t\t\tif ('minNumSamples' in t.tw) return t.tw.minNumSamples <= t.counts.samples\n\t\t\t\tif (!grp.settings) return true\n\t\t\t\treturn !('minNumSamples' in grp.settings) || t.counts.samples >= grp.settings.minNumSamples\n\t\t\t})\n\t\t\t/*\n                NOTE: When sorting terms by sample counts, those counts would have been computed before applying the s.maxSample truncation.\n                The sample counts are then re-computed, if applicable, in setSampleCountByTerm() after sample list truncation.\n                If the left-most sample group does not have much less hits relative to sample groups to its right, then this\n                may look like a term with less sample count got mistakenly sorted to the top.\n\n                TODO: \n                (a) Option for s.sortSampleGroupBy = hits-by-term-order, and force this option so that the left-most sample group would\n                    make visually sense with s.maxSample is not empty and s.sortTermsBy = 'sampleCount'\n                (b) OR, re-sort the term lst based on sample counts without rearranging sample groups\n            */\n\t\t\t.sort(termSorter)\n\n\t\tif (!processedLst.length) continue\n\t\tfor (const [index, t] of processedLst.entries()) {\n\t\t\tconst { tw, counts } = t\n\t\t\tconst ref = data.refs.byTermId[t.tw.$id] || {}\n\t\t\ttermOrder.push({\n\t\t\t\tgrp,\n\t\t\t\tgrpIndex,\n\t\t\t\tvisibleGrpIndex,\n\t\t\t\ttw,\n\t\t\t\tindex, // rendered index\n\t\t\t\tlstIndex: t.index, // as-listed index, before applying term filters\n\t\t\t\tprocessedLst,\n\t\t\t\tprevGrpTotalIndex: totalIndex,\n\t\t\t\ttotalIndex: totalIndex + index,\n\t\t\t\tref,\n\t\t\t\tallCounts: counts\n\t\t\t\t// note: term label will be assigned after sample counts are known\n\t\t\t\t// label: t.tw.label || t.tw.term.name,\n\t\t\t})\n\t\t}\n\n\t\ttotalIndex += processedLst.length\n\t\tvisibleGrpIndex += 1\n\t}\n\tthis.numTerms = termOrder.length\n\tthis.numClusterTerms = numClusterTerms\n\treturn termOrder\n}\n\nexport function getSampleGroups(data) {\n\tconst s = this.settings.matrix\n\tconst defaultSampleGrp = {\n\t\tid: this.config.divideBy?.$id,\n\t\tname: this.config.divideBy ? 'Not annotated' : '',\n\t\tlst: []\n\t}\n\tconst sampleGroups = new Map()\n\tconst term = this.config.divideBy?.term || {}\n\tconst $id = this.config.divideBy?.$id || '-'\n\tconst exclude = this.config.divideBy?.exclude || []\n\tconst values = term.values || {}\n\tconst ref = data.refs.byTermId[$id] || {}\n\n\tfor (const row of data.lst) {\n\t\tif ($id in row) {\n\t\t\t// a membership multivalue divideBy cell may carry multiple {key} entries;\n\t\t\t// the sample then appears in the group of each category it belongs to,\n\t\t\t// same as the barchart/violin divide-by behavior\n\t\t\tconst cell = row[$id]\n\t\t\tconst keys = term.type == 'multivalue' && Array.isArray(cell.values) ? cell.values.map(v => v.key) : [cell.key]\n\t\t\tfor (const key of keys) {\n\t\t\t\tconst name = key in values && values[key].label ? values[key].label : key\n\t\t\t\tif (!sampleGroups.has(key)) {\n\t\t\t\t\tconst grp = {\n\t\t\t\t\t\tname: `${name}`, // convert to a string\n\t\t\t\t\t\tid: key,\n\t\t\t\t\t\tlst: [],\n\t\t\t\t\t\ttw: this.config.divideBy,\n\t\t\t\t\t\tlegendGroups: {},\n\t\t\t\t\t\tisExcluded: exclude.includes(key)\n\t\t\t\t\t}\n\t\t\t\t\tif (ref.bins && s.sortSampleGrpsBy == 'name') grp.order = ref.bins.findIndex(bin => bin.name == key)\n\t\t\t\t\telse delete grp.order\n\t\t\t\t\tsampleGroups.set(key, grp)\n\t\t\t\t}\n\t\t\t\tsampleGroups.get(key).lst.push(row)\n\t\t\t}\n\t\t} else {\n\t\t\tdefaultSampleGrp.lst.push(row)\n\t\t}\n\t}\n\n\tconst sampleGrpsArr = [...sampleGroups.values()]\n\tconst n = sampleGroups.size\n\tif (n > 100 && sampleGrpsArr.filter(sg => sg.lst.length < 3).length > 0.8 * n) {\n\t\tconst l = s.controlLabels\n\t\tthrow `Did not group ${l.samples} by \"${term.name}\": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`\n\t}\n\n\tif (defaultSampleGrp.lst.length && !sampleGroups.size) {\n\t\tsampleGroups.set(undefined, defaultSampleGrp)\n\t\tsampleGrpsArr.push(...sampleGroups.values())\n\t}\n\tthis.asListedSampleOrder = []\n\tfor (const grp of sampleGrpsArr) {\n\t\tthis.asListedSampleOrder.push(...grp.lst.map(s => s.sample))\n\t}\n\tconst selectedDictTerms = this.termOrder.filter(t => t.tw.sortSamples && t.tw.term.type != 'geneVariant')\n\t// initial sorting for ungrouped samples, prioritizes grouping by gene variant, skippin other sorters at this step\n\tconst noGrpSampleSorter = getSampleSorter(this, s, data.lst, {\n\t\tskipSorter: (p, tw) => !p.types?.includes('geneVariant') && selectedDictTerms.find(t => t.tw.$id === tw.$id)\n\t})\n\tconst noGrpSampleOrder = data.lst.sort(noGrpSampleSorter)\n\t// truncate the samples based on the initial sorting\n\tconst allowedSamples = noGrpSampleOrder.slice(0, s.maxSample)\n\t// do not include samples that are not in the truncated allowedSamples\n\tconst dataFilter = d => allowedSamples.includes(d)\n\t// these hits counter functions may be used for sortSampleGrpsBy = 'hits'\n\tconst hitsPerSample = (t, c) => t + (typeof c == 'object' && c.countedValues?.length ? 1 : 0)\n\tconst countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0)\n\t// this second sorter will be applied within each group of samples\n\tconst grpLstSampleSorter = getSampleSorter(this, s, data.lst)\n\tfor (const grp of sampleGrpsArr) {\n\t\tgrp.lst = grp.lst.filter(dataFilter)\n\t\tgrp.totalCountedValues = grp.lst.reduce(countHits, 0)\n\t\tgrp.lst.sort(grpLstSampleSorter)\n\t}\n\tconst sampleGrpSorter = getSampleGroupSorter(this)\n\treturn sampleGrpsArr.sort(sampleGrpSorter)\n}\n\nexport function getSampleOrder(data) {\n\tconst s = this.settings.matrix\n\tthis.visibleSampleGrps = new Set()\n\tconst sampleOrder = []\n\tlet total = 0,\n\t\tnumHiddenGrps = 0\n\tfor (const [grpIndex, grp] of this.sampleGroups.entries()) {\n\t\tif (!grp.lst.length) continue\n\t\tif (grp.isExcluded) numHiddenGrps++\n\t\tlet processedLst = grp.lst\n\t\tfor (const [index, row] of processedLst.entries()) {\n\t\t\tsampleOrder.push({\n\t\t\t\tgrp,\n\t\t\t\tgrpIndex: grpIndex - numHiddenGrps, // : this.sampleGroups.length,\n\t\t\t\trow,\n\t\t\t\tindex,\n\t\t\t\tprevGrpTotalIndex: total,\n\t\t\t\ttotalIndex: total + index,\n\t\t\t\ttotalHtAdjustments: 0, // may be required when transposed???\n\t\t\t\tgrpTotals: { htAdjustment: 0 }, // may be required when transposed???\n\t\t\t\tprocessedLst\n\t\t\t})\n\t\t}\n\t\tif (!grp.isExcluded) total += processedLst.length\n\t\tthis.visibleSampleGrps.add(grp)\n\t\t//if (s.maxSample && total >= s.maxSample) break // *** Apply group sorting before column truncation ????? ****\n\t}\n\tthis.unfilteredSampleOrder = sampleOrder\n\treturn sampleOrder.filter(so => !so.grp.isExcluded)\n}\n\n/*\nGiven the anno of a term for a sample, generate the \n    filteredValues (values matched the filter)\n    countedValues (values counted, Class = Blank or WT are not counted)\n    renderedValues (values rendered on matrix)\n*/\nexport function classifyValues(anno, tw, grp, s, sample) {\n\tconst values = 'value' in anno ? [anno.value] : anno.values\n\tif (!values) return { filteredValues: null, countedValues: null, renderedValues: null }\n\n\t// isSpecific is the filter that is specific to the term\n\tconst isSpecific = [tw.valueFilter || grp.valueFilter].filter(v => v && true)\n\tif (isSpecific.length && isSpecific[0].type !== 'tvs' && isSpecific[0].type !== 'tvslst')\n\t\tthrow `unknown matrix value filter type='${isSpecific.type}'`\n\n\t// filteredValues are the values passed the isSpecific filter\n\tlet filteredValues = !isSpecific.length\n\t\t? values\n\t\t: values.filter(v => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample))\n\n\tconst renderedValues = []\n\tif (tw.term.type == 'geneVariant' && tw.q?.type == 'values') {\n\t\t// filteredValues.sort((a, b) => getMclassOrder(a) - getMclassOrder(b))\n\t\tfilteredValues.sort(this.mclassSorter)\n\n\t\tif (s.cellEncoding == '') renderedValues.push(...filteredValues)\n\t\telse {\n\t\t\tconst sortedFilteredValues = []\n\t\t\t// dt=1 are SNVindels, dt=4 CNV, dt=3 Gene Expression\n\t\t\t// will render only one matching value per dt\n\t\t\tfor (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {\n\t\t\t\tconst v =\n\t\t\t\t\tdt == dtgeneexpression\n\t\t\t\t\t\t? filteredValues.find(v => v.dt === dt)\n\t\t\t\t\t\t: filteredValues.find(v => v.dt === dt && v.class !== 'WT' && v.class !== 'Blank')\n\t\t\t\tif (v) renderedValues.push(v)\n\n\t\t\t\tconst oneDtV = filteredValues.filter(v => v.dt === dt)\n\t\t\t\tsortedFilteredValues.push(...oneDtV)\n\t\t\t}\n\t\t\tfilteredValues = sortedFilteredValues\n\t\t}\n\t} else {\n\t\trenderedValues.push(...filteredValues)\n\t}\n\n\t// group stacked cell values to avoid striped pattern\n\t// if (tw.term.type == 'geneVariant') {\n\t// renderedValues.sort(this.stackSiblingCellsByClass)\n\t// filteredValues.sort(this.stackSiblingCellsByClass)\n\t// }\n\n\treturn {\n\t\tfilteredValues,\n\t\tcountedValues: filteredValues.filter(v => {\n\t\t\tif (tw.term.type == 'geneVariant') {\n\t\t\t\tif (tw.q?.type == 'predefined-groupset' || tw.q?.type == 'custom-groupset') {\n\t\t\t\t\t// groupsetting in use\n\t\t\t\t\t// values are group assignments\n\t\t\t\t\t// only count assignments to group with highest\n\t\t\t\t\t// priority in groupset\n\t\t\t\t\tconst groupset =\n\t\t\t\t\t\ttw.q.type == 'predefined-groupset' ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset\n\t\t\t\t\tif (!groupset) throw 'groupset not found'\n\t\t\t\t\tconst group = groupset.groups[0]\n\t\t\t\t\tif (v != group.name) return false\n\t\t\t\t} else {\n\t\t\t\t\t// groupsetting not in use\n\t\t\t\t\t// values are mutation classes\n\t\t\t\t\t// do not count WT, blank, or skipped classes\n\t\t\t\t\tif (v.class == 'WT' || v.class == 'Blank' || s.geneVariantCountSamplesSkipMclass.includes(v.class))\n\t\t\t\t\t\treturn false\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn true\n\t\t}),\n\t\trenderedValues\n\t}\n}\n\nexport function stackSiblingCellsByClass(a, b) {\n\treturn a.class === b.class ? 0 : a.class === 'Blank' ? 1 : b.class == 'Blank' ? -1 : a.class < b.class ? -1 : 1\n}\n"],
-  "mappings": 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-  "names": ["v", "s"]
-}

package/dist/chunk-JPQSDB2H.js

@@ -1,102 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-I56CSICA.js";
-import {
-  fillTermWrapper
-} from "./chunk-GQQ4R6BI.js";
-import {
-  dictionaryNumericTypes,
-  numericTypes
-} from "./chunk-7UFK4GVI.js";
-import {
-  copyMerge
-} from "./chunk-H6INPPUC.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-JPQSDB2H.js.map