@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/chunk-WIQVSCD5.js

@@ -0,0 +1,294 @@
+import {
+  getSortOptions
+} from "./chunk-AR3HXZIW.js";
+import {
+  defaultUiLabels,
+  fillTermWrapper
+} from "./chunk-C3HEDQPT.js";
+import {
+  isDictionaryType
+} from "./chunk-3XBG5HIV.js";
+import {
+  CNVClasses,
+  dtcnv,
+  mclass,
+  mutationClasses,
+  proteinChangingMutations,
+  synonymousMutations,
+  truncatingMutations
+} from "./chunk-SB36AUG7.js";
+import {
+  copyMerge
+} from "./chunk-WINIL2KN.js";
+
+// plots/matrix/matrix.config.js
+async function getPlotConfig(opts = {}, app) {
+  const controlLabels = structuredClone(defaultUiLabels);
+  const devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio;
+  const config = {
+    // data configuration
+    termgroups: [],
+    samplegroups: [],
+    divideBy: null,
+    legendValueFilter: {
+      isAtomic: true,
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: []
+    },
+    legendGrpFilter: {
+      isAtomic: true,
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: []
+    },
+    filter: {
+      isAtomic: true,
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: []
+    },
+    // cnvCutoffs: {},
+    // rendering options
+    settings: {
+      matrix: {
+        svgCanvasSwitch: 1e3,
+        // the number of samples to trigger switching between svg and canvas
+        useMinPixelWidth: true,
+        // canvas may be hazy if false, but more accurately reflects column density
+        cellEncoding: "",
+        // can be "oncoprint" | "stacked" | "single"
+        margin: {
+          top: 10,
+          right: 5,
+          bottom: 20,
+          left: 50
+        },
+        // set any dataset-defined sample limits and sort priority, otherwise undefined
+        // put in settings, so that later may be overridden by a user
+        maxGenes: opts.settings?.maxGenes || 50,
+        maxSample: opts.settings?.maxSample || 1e3,
+        sampleNameFilter: "",
+        sortSamplesBy: "a",
+        sortPriority: void 0,
+        // will be filled-in
+        sortBySampleAncestry: app.vocabApi.termdbConfig.hasSampleAncestry ? "last" : false,
+        // indicates sorting priority by sample ancestry
+        // sortByMutation: 'consequence', computed
+        // sortByCNV: true, computed
+        //sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),
+        sortSampleGrpsBy: "name",
+        // 'hits' | 'name' | 'sampleCount'
+        sortSamplesTieBreakers: [{
+          $id: "sample",
+          sortSamples: {}
+          /*split: {char: '', index: 0}*/
+        }],
+        sortTermsBy: "sampleCount",
+        // or 'as listed'
+        // do not show number of samples at hiercluster gene row labels
+        samplecount4gene: opts.chartType == "hierCluster" ? "" : "abs",
+        //true, // 'abs' (default, previously true), 'pct', ''  (previously false)
+        geneVariantCountSamplesSkipMclass: [],
+        cellbg: "#ececec",
+        showGrid: "",
+        // false | 'pattern' | 'rect'
+        // whether to show these controls buttons
+        addMutationCNVButtons: false,
+        truncatingMutations,
+        proteinChangingMutations,
+        synonymousMutations,
+        mutationClasses,
+        CNVClasses,
+        gridStroke: "#fff",
+        outlineStroke: "#ccc",
+        beamStroke: "#f00",
+        colw: 0,
+        colwMin: 0.1 / devicePixelRatio,
+        colwMax: 16,
+        colspace: 1,
+        colgspace: 8,
+        colglabelpos: true,
+        collabelpos: "bottom",
+        collabelvisible: true,
+        collabelgap: 5,
+        collabelpad: 1,
+        collabelmaxchars: 32,
+        rowh: 18,
+        //use 0 to auto-compute row height, previous default=18,
+        rowhMin: 1,
+        rowhMax: 20,
+        rowspace: 1,
+        rowgspace: 8,
+        rowlabelpos: "left",
+        // | 'right'
+        rowlabelgap: 5,
+        rowlabelvisible: true,
+        rowlabelpad: 1,
+        rowlabelmaxchars: 32,
+        legendGrpLabelMaxChars: 26,
+        grpLabelFontSize: 12,
+        minLabelFontSize: 6,
+        maxLabelFontSize: 14,
+        transpose: false,
+        // 'auto' shows column labels only when columns are wide enough (colw >= minLabelFontSize);
+        sampleLabelsToggle: "auto",
+        // 'auto' | 'hide'
+        sampleLabelOffset: 120,
+        sampleGrpLabelOffset: 120,
+        sampleGrpLabelMaxChars: 32,
+        termLabelOffset: 80,
+        termGrpLabelOffset: 80,
+        termGrpLabelMaxChars: 32,
+        duration: 0,
+        zoomLevel: 1,
+        zoomCenterPct: 0,
+        zoomIndex: 0,
+        zoomGrpIndex: 0,
+        zoomMin: 0.5,
+        zoomIncrement: 0.1,
+        zoomStep: 1,
+        // renderedWMax should not be exposed as a user-input
+        // 60000 pixels is based on laptop and external monitor tests,
+        // when a canvas dataURL image in a zoomed-in matrix svg stops rendering
+        imgWMax: 6e4 / devicePixelRatio,
+        scrollHeight: 12,
+        controlLabels,
+        cnvUnit: "log2ratio",
+        ignoreCnvValues: false,
+        //will ignore numeric CNV values if true
+        barh: 32,
+        // default bar height for continuous terms,
+        // possible string entries:
+        // - "genesetEdit", for gene-centric embedders only like GDC OncoMatrix
+        // - may add other optional hints later
+        showHints: [],
+        genesetEditUiVersion: "",
+        // '' | 'withTabs'
+        // settings for a specific tw
+        twSpecificSettings: {},
+        oncoPrintSNVindelCellBorder: false,
+        // whether to show white cell border for SNVindel in oncoPrint mode
+        cnvValues: {
+          //Properties match the args for the ColorScales
+          //numericInput arg
+          cutoffMode: "percentile",
+          defaultPercentile: 99,
+          min: null,
+          max: null,
+          percentile: 99
+        }
+      }
+    }
+  };
+  const s = config.settings;
+  const fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12);
+  s.legend = {
+    ontop: false,
+    lineh: 25,
+    padx: 5,
+    padleft: 0,
+    //150,
+    padright: 20,
+    padbtm: 30,
+    fontsize,
+    iconh: fontsize - 2,
+    iconw: fontsize - 2,
+    hangleft: 1,
+    linesep: false
+  };
+  const overrides = app.vocabApi.termdbConfig.matrix || {};
+  copyMerge(config.settings.matrix, overrides.settings);
+  if (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter;
+  if (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter;
+  if (overrides.filter) config.filter = overrides.filter;
+  if (opts.name) {
+    const data = await app.vocabApi.getMatrixByName(opts.name);
+    if (!data) throw "error from getMatrixByName()";
+    if (data.error) throw data.error;
+    copyMerge(config, data);
+  }
+  const os = opts?.settings?.matrix;
+  if (os) {
+    if ((os.sortSamplesBy == "custom" || os.sortSamplesBy == "asListed") && os.sortOptions?.custom.label == "against alteration type") {
+      os.sortSamplesBy = "a";
+    }
+    if (os.sortOptions) {
+      delete os.sortOptions.custom;
+      delete os.sortOptions.asListed;
+    }
+  }
+  copyMerge(config, opts);
+  const m = config.settings.matrix;
+  m.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m);
+  m.duration = 0;
+  m.colw = 0;
+  if (m.sortSamplesBy != "asListed" && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = "a";
+  else if (["selectedTerms", "class", "dt", "hits"].includes(m.sortSamplesBy)) m.sortSamplesBy = "a";
+  if (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = "abs";
+  if (window.location.hostname == "localhost") {
+    if (window.location.hash == "#canvas") m.svgCanvasSwitch = 0;
+  }
+  for (const grp of config.termgroups) {
+    const promises = [];
+    for (const tw of grp.lst) {
+      if (!tw.term?.type || isDictionaryType(tw.term.type)) {
+        if (!tw.id && tw.term.type != "samplelst" && tw.term.type != "termCollection") {
+          if (!tw.term.id) throw `missing tw.id and tw.term.id`;
+          tw.id = tw.term.id;
+        }
+        if (tw.term?.type != "samplelst" && tw.term?.type != "termCollection") delete tw.term;
+      }
+      promises.push(fillTermWrapper(tw, app.vocabApi));
+    }
+    grp.lst = await Promise.all(promises);
+  }
+  if (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi);
+  return config;
+}
+function setComputedConfig(config) {
+  const s = config.settings.matrix;
+  const allClasses = [...s.mutationClasses, ...s.CNVClasses];
+  s.filterByClass = { isAtomic: true };
+  for (const f of config.legendGrpFilter.lst) {
+    if (!f.dt) continue;
+    allClasses.filter((m) => f.dt.includes(mclass[m].dt)).forEach((key2) => {
+      s.filterByClass[key2] = "value";
+    });
+  }
+  for (const f of config.legendValueFilter.lst) {
+    if (!f.legendGrpName || f.tvs?.term?.type !== "geneVariant") continue;
+    if (f.tvs.values?.[0].mclasslst)
+      f.tvs.values[0].mclasslst.forEach((key2) => {
+        s.filterByClass[key2] = f.legendFilterType?.endsWith("_hard") ? "case" : "value";
+      });
+    else if (f.tvs.values)
+      f.tvs.values.forEach((v) => {
+        s.filterByClass[key] = "value";
+      });
+    else throw `unhandled tvs from legendValueFilter`;
+  }
+  s.hiddenVariants = Object.keys(s.filterByClass).filter((c) => c !== "isAtomic");
+  const hiddenCNVs = new Set(s.hiddenVariants.filter((key2) => mclass[key2]?.dt === dtcnv));
+  s.hiddenCNVs = [...hiddenCNVs];
+  s.showMatrixCNV = !hiddenCNVs.size ? "all" : hiddenCNVs.size == s.CNVClasses.length ? "none" : "bySelection";
+  s.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length;
+  const hiddenMutations = new Set(s.hiddenVariants.filter((key2) => s.mutationClasses.find((k) => k === key2)));
+  s.hiddenMutations = [...hiddenMutations];
+  const PCset = new Set(s.proteinChangingMutations);
+  const TMset = new Set(s.truncatingMutations);
+  s.showMatrixMutation = !hiddenMutations.size ? "all" : hiddenMutations.size == s.mutationClasses.length ? "none" : hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every((m) => !PCset.has(m)) ? "onlyPC" : hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every((m) => !TMset.has(m)) ? "onlyTruncating" : "bySelection";
+  s.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length;
+  const tiebreakers = s.sortOptions.a?.sortPriority.find((sp) => sp.types.length == 1 && sp.types[0] == "geneVariant")?.tiebreakers || [];
+  s.sortByMutation = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 1)?.isOrdered ? "consequence" : "presence";
+  s.sortByCNV = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 4)?.disabled !== true;
+}
+
+export {
+  getPlotConfig,
+  setComputedConfig
+};
+//# sourceMappingURL=chunk-WIQVSCD5.js.map

package/dist/chunk-WXXRVJSP.js

@@ -0,0 +1,56 @@
+import {
+  sayerror
+} from "./chunk-C3HEDQPT.js";
+import {
+  TermTypeGroups
+} from "./chunk-SB36AUG7.js";
+
+// termdb/handlers/singleCellCellType.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.validateOpts(opts);
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
+    if (!scctTerms?.length) {
+      sayerror(
+        holder,
+        `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
+      );
+      return;
+    }
+    const usecaseConfig = opts.usecase?.specialCase?.config;
+    const plots = usecaseConfig?.sample?.plots;
+    const isMeta = usecaseConfig?.sample?.isMetaResult;
+    const filtered = plots ? scctTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scctTerms.filter((t) => t.plot === usecaseConfig.name) : scctTerms;
+    const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${t.name} (${t.plot})`;
+    const filteredTerms = new Set(
+      plots || !usecaseConfig?.name ? filtered.map((t) => ({ ...t, label: getLabel(t) })) : filtered
+    );
+    for (const t of Array.from(filteredTerms)) {
+      holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
+        const term = this.makeTerm(t, usecaseConfig);
+        this.callback(term);
+      });
+    }
+  }
+  makeTerm(_term, usecaseConfig) {
+    const term = { ..._term };
+    if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
+    return term;
+  }
+  validateOpts(opts) {
+    if (opts.callback == null) throw new Error("callback is required");
+    if (opts.app == null) throw new Error("app is required");
+    if (opts.holder == null) throw new Error("holder is required");
+    if (opts.usecase == null) throw new Error("usecase is required");
+    if (!opts.app.vocabApi.termdbConfig?.termType2terms)
+      throw new Error("termType2terms is required in termdbConfig for singleCellCellType handler");
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-WXXRVJSP.js.map

package/dist/chunk-X4MV2M5F.js

@@ -0,0 +1,129 @@
+import {
+  keyupEnter
+} from "./chunk-C3HEDQPT.js";
+
+// src/block.mds.svcnv.share.js
+function rnabamtk_initparam(c) {
+  if (!c.dna_mintotalreads) c.dna_mintotalreads = 8;
+  if (!c.rna_mintotalreads) c.rna_mintotalreads = 8;
+  if (!c.hetsnp_minbaf) c.hetsnp_minbaf = 0.3;
+  if (!c.hetsnp_maxbaf) c.hetsnp_maxbaf = 0.7;
+  if (c.rnapileup_q == void 0) c.rnapileup_q = 0;
+  if (!c.rnapileup_Q) c.rnapileup_Q = 13;
+  if (!c.binompvaluecutoff) c.binompvaluecutoff = 0.05;
+  if (!c.clientcolor_snpinuse) c.clientcolor_snpinuse = "blue";
+  if (!c.clientcolor_markernotinuse) c.clientcolor_markernotinuse = "#bbb";
+}
+function configPanel_rnabam(tk, block, loadTk) {
+  const c = tk.checkrnabam;
+  if (!c) return;
+  tk.tkconfigtip.d.append("hr");
+  const d = tk.tkconfigtip.d.append("div").style("margin", "15px 0px");
+  d.append("div").style("opacity", 0.5).style("font-size", ".9em").text("Finding heterozygous SNPs in DNA");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("DNA minimum total read count ");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.dna_mintotalreads).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.dna_mintotalreads == v) {
+        return;
+      }
+      c.dna_mintotalreads = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total coverage is below cutoff, it will be skipped.");
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Heterozygous SNP BAF range&nbsp;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_minbaf).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.hetsnp_minbaf == v) {
+        return;
+      }
+      c.hetsnp_minbaf = v;
+      loadTk(tk, block);
+    });
+    row.append("span").style("opacity", ".5").style("font-size", ".8em").html("&nbsp;&leq; BAF &leq;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_maxbaf).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.hetsnp_maxbaf == v) {
+        return;
+      }
+      c.hetsnp_maxbaf = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's BAF (B-allele fraction) is within this range, it is heterozygous.");
+  }
+  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Counting alleles in RNA-seq BAM file");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Skip alignments with mapQ smaller than&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_q).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v < 0) return;
+      if (c.rnapileup_q == v) {
+        return;
+      }
+      c.rnapileup_q = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Skip bases with baseQ/BAQ smaller than&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_Q).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.rnapileup_Q == v) {
+        return;
+      }
+      c.rnapileup_Q = v;
+      loadTk(tk, block);
+    });
+  }
+  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Binomial test on whether a heterozygous SNP shows allelic bias in RNA");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("P-value cutoff&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.binompvaluecutoff).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0 || v >= 1) return;
+      if (c.binompvaluecutoff == v) {
+        return;
+      }
+      c.binompvaluecutoff = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("RNA minimum total read count&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rna_mintotalreads).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.rna_mintotalreads == v) {
+        return;
+      }
+      c.rna_mintotalreads = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total read count from RNA is below cutoff, it won't do binomial test.");
+  }
+}
+
+export {
+  rnabamtk_initparam,
+  configPanel_rnabam
+};
+//# sourceMappingURL=chunk-X4MV2M5F.js.map