@sjcrh/proteinpaint-client 2.190.2 → 2.191.0

package/dist/chunk-WMELUFVS.js

@@ -0,0 +1,254 @@
+import {
+  getMclassSorter,
+  getSampleGroupSorter,
+  getSampleSorter,
+  getTermSorter
+} from "./chunk-VXKO2ONI.js";
+import {
+  sample_match_termvaluesetting
+} from "./chunk-7IYJZZQI.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel
+} from "./chunk-EBKERML3.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 key = row[$id].key;
+      const name = key in values && values[key].label ? values[key].label : key;
+      if (!sampleGroups.has(key)) {
+        const grp = {
+          name: `${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-WMELUFVS.js.map

package/dist/chunk-WS3NUPNV.js

@@ -0,0 +1,119 @@
+import {
+  GENE_EXPRESSION,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-TVADJLMF.js";
+
+// common/termutils.js
+function sample_match_termvaluesetting(row, filter, geneVariant$ids) {
+  const lst = !filter ? [] : filter.type == "tvslst" ? filter.lst : [filter];
+  let numberofmatchedterms = 0;
+  for (const item of lst) {
+    if (item.type == "tvslst") {
+      if (sample_match_termvaluesetting(row, item)) {
+        numberofmatchedterms++;
+      }
+    } else {
+      const t = item.tvs;
+      let samplevalue;
+      if (t.term.type == "geneVariant") {
+        samplevalue = geneVariant$ids.map((g) => row[g]).filter((s) => s);
+      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
+        samplevalue = row[t.term.id] || row[t.term.$id]?.key;
+      } else if (t.term.type == "survival") {
+        samplevalue = row[t.term.$id]?.key;
+      } else {
+        samplevalue = row[t.term.id] || row[t.term.$id]?.value;
+      }
+      let thistermmatch;
+      if (t.term.type == "categorical") {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
+        thistermmatch = valueset.has(samplevalue);
+      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        for (const range of t.ranges) {
+          if ("value" in range) {
+            thistermmatch = samplevalue === range.value;
+            if (thistermmatch) break;
+          } else if (samplevalue == range.name) {
+            thistermmatch = true;
+            break;
+          } else {
+            if (t.term.values) {
+              const v = t.term.values[samplevalue.toString()];
+              if (v && v.uncomputable) {
+                continue;
+              }
+            }
+            let left, right;
+            if (range.startunbounded) {
+              left = true;
+            } else if ("start" in range) {
+              if (range.startinclusive) {
+                left = samplevalue >= range.start;
+              } else {
+                left = samplevalue > range.start;
+              }
+            }
+            if (range.stopunbounded) {
+              right = true;
+            } else if ("stop" in range) {
+              if (range.stopinclusive) {
+                right = samplevalue <= range.stop;
+              } else {
+                right = samplevalue < range.stop;
+              }
+            }
+            thistermmatch = left && right;
+          }
+          if (thistermmatch) break;
+        }
+      } else if (t.term.type == "condition") {
+        const key = getPrecomputedKey(t);
+        const anno = samplevalue && samplevalue[key];
+        if (anno) {
+          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
+        }
+      } else if (t.term.type == "survival") {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
+        thistermmatch = valueset.has(samplevalue);
+      } else if (t.term.type == "geneVariant" && t.legendFilterType == "geneVariant_hard") {
+        const f = t.values[0];
+        thistermmatch = samplevalue.find((s) => {
+          for (const v of s.values) {
+            if (v.dt == f.dt && (!v.origin || v.origin == f.origin) && f.mclasslst.includes(v.class)) return true;
+          }
+        }) && true;
+      } else if (t.term.type == SINGLECELL_GENE_EXPRESSION) {
+      } else {
+        throw "unknown term type";
+      }
+      if (t.isnot) {
+        thistermmatch = !thistermmatch;
+      }
+      if (thistermmatch) numberofmatchedterms++;
+    }
+    if (filter.join == "or" && numberofmatchedterms) return true;
+  }
+  if (numberofmatchedterms == lst.length) return true;
+}
+
+export {
+  sample_match_termvaluesetting
+};
+//# sourceMappingURL=chunk-WS3NUPNV.js.map