@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/chunk-VH5W6ODW.js

@@ -0,0 +1,294 @@
+import {
+  getSortOptions
+} from "./chunk-XQYDXA47.js";
+import {
+  defaultUiLabels,
+  fillTermWrapper
+} from "./chunk-55FABQU2.js";
+import {
+  isDictionaryType
+} from "./chunk-KIAMLQ7S.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-VH5W6ODW.js.map

package/dist/chunk-VROF55EH.js

@@ -0,0 +1,255 @@
+import {
+  first_genetrack_tolist
+} from "./chunk-55FABQU2.js";
+import {
+  HYPER_COLOR,
+  HYPO_COLOR
+} from "./chunk-VA57CUC7.js";
+
+// plots/dmr/settings/defaults.ts
+function getDefaultDMRSettings(opts) {
+  const overrides = opts.settings || {};
+  const dm = opts?.app?.vocabApi?.termdbConfig?.queries?.dnaMethylation;
+  const chr = opts?.coordinateOverride?.chr;
+  const elementScale = dm?.regionAnalysis == "element" || Array.isArray(dm?.cpgChroms) && !!chr && !dm.cpgChroms.includes(chr);
+  const defaults = {
+    blockWidth: 800,
+    pad: elementScale ? 1e5 : 2e3,
+    lambda: elementScale ? 5e4 : 1e3,
+    C: 2,
+    fdr_cutoff: 0.05,
+    colors: {
+      group1: "#3b5ee6",
+      group2: "#c04e00",
+      hyper: HYPER_COLOR,
+      hypo: HYPO_COLOR
+    },
+    maxLoessRegion: 25e4,
+    minProbesForCi: 10,
+    backend: "rust",
+    maxRegionSize: 5e6
+  };
+  if (overrides.colors) {
+    Object.assign(defaults.colors, overrides.colors);
+    delete overrides.colors;
+  }
+  return Object.assign(defaults, overrides);
+}
+
+// plots/dmr/viewModel/DmrViewModel.ts
+var CCRE_TRACK_NAME = "ENCODE cCREs";
+var DmrViewModel = class {
+  constructor(dmrResult, config, genomeObj, queryChr, queryStart, queryStop) {
+    const { settings } = config;
+    const dmrBedItems = this.makeDmrBedItems(dmrResult, settings);
+    const sigCpgBedItems = this.makeSigCpgBedItems(dmrResult, settings, queryChr, queryStart, queryStop);
+    const xRange = (queryStop ?? 0) - (queryStart ?? 0);
+    const loess = dmrResult.diagnostic?.loess;
+    const showLoess = !!(loess && loess.group1_fitted.length > 0 && loess.group2_fitted.length > 0);
+    const showDots = xRange <= settings.dmr.maxLoessRegion;
+    const betaTrackResult = dmrResult.diagnostic ? this.renderBetaTrack(
+      dmrResult.diagnostic,
+      config,
+      settings.dmr.blockWidth,
+      showLoess,
+      showDots,
+      queryStart,
+      queryStop
+    ) : void 0;
+    this.viewData = {
+      tklst: this.buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackResult?.img),
+      legendRows: this.buildLegendData(
+        config,
+        dmrResult.dmrs,
+        sigCpgBedItems,
+        showLoess,
+        showDots,
+        betaTrackResult?.showCi ?? false
+      ),
+      diagnostic: dmrResult.diagnostic,
+      dmrs: dmrResult.dmrs,
+      dmrBedItems,
+      showLoess,
+      showDots
+    };
+  }
+  buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackImg) {
+    const tklst = [];
+    first_genetrack_tolist(genomeObj, tklst);
+    const ccre = (genomeObj?.tracks || []).find((t) => t.name == CCRE_TRACK_NAME);
+    if (ccre) tklst.push(structuredClone(ccre));
+    tklst.push({ type: "bedj", name: "DMRs", bedItems: dmrBedItems });
+    tklst.push({ type: "bedj", name: "Sig. CpGs", bedItems: sigCpgBedItems });
+    if (betaTrackImg) {
+      tklst.push({
+        type: "bigwig",
+        name: "Per-CpG Means",
+        height: 150,
+        imgData: betaTrackImg
+      });
+    }
+    return tklst;
+  }
+  buildLegendData(config, dmrs, sigCpgBedItems, showLoess, showDots, showCi) {
+    const { colors } = config.settings.dmr;
+    const g1 = config.group1Name || "Group 1";
+    const g2 = config.group2Name || "Group 2";
+    const meansItems = [];
+    if (showDots) {
+      meansItems.push({ text: `${g1} (control)`, color: colors.group1 }, { text: `${g2} (case)`, color: colors.group2 });
+    }
+    if (showLoess) {
+      const ciLabel = showCi ? " + 95% CI" : "";
+      meansItems.push(
+        { text: `${g1} LOESS trend${ciLabel}`, color: colors.group1, style: showCi ? "shaded" : "dashed" },
+        { text: `${g2} LOESS trend${ciLabel}`, color: colors.group2, style: showCi ? "shaded" : "dashed" }
+      );
+    }
+    const rows = [{ label: "Per-CpG Means", items: meansItems }];
+    const hasHyper = dmrs.some((d) => d.direction === "hyper");
+    const hasHypo = dmrs.some((d) => d.direction === "hypo");
+    if (hasHyper || hasHypo) {
+      const items = [];
+      if (hasHyper) items.push({ text: "Hypermethylated", color: colors.hyper });
+      if (hasHypo) items.push({ text: "Hypomethylated", color: colors.hypo });
+      rows.push({ label: "DMR", items });
+    }
+    if (sigCpgBedItems.length) {
+      const items = [];
+      const hasHyperCpg = sigCpgBedItems.some((b) => b.color === colors.hyper);
+      const hasHypoCpg = sigCpgBedItems.some((b) => b.color === colors.hypo);
+      if (hasHyperCpg) items.push({ text: "Hyper (FDR sig.)", color: colors.hyper });
+      if (hasHypoCpg) items.push({ text: "Hypo (FDR sig.)", color: colors.hypo });
+      rows.push({ label: "Sig. CpGs", items });
+    }
+    return rows;
+  }
+  /**
+   * Render the per-CpG means scatter plot to an offscreen canvas and return
+   * a data URI suitable for the bigwig imgData track.
+   */
+  renderBetaTrack(diagnostic, config, blockWidth, showLoess, showDots, queryStart, queryStop) {
+    const { probes } = diagnostic;
+    if (!probes.positions.length) return void 0;
+    const { colors, fdr_cutoff, minProbesForCi } = config.settings.dmr;
+    const dpr = typeof window !== "undefined" && window.devicePixelRatio > 1 ? window.devicePixelRatio : 1;
+    const width = blockWidth;
+    const height = 150;
+    const canvas = document.createElement("canvas");
+    canvas.width = width * dpr;
+    canvas.height = height * dpr;
+    const ctx = canvas.getContext("2d");
+    if (!ctx) return void 0;
+    ctx.scale(dpr, dpr);
+    const xMin = queryStart ?? probes.positions[0];
+    const xMax = queryStop ?? probes.positions[probes.positions.length - 1];
+    const xRange = xMax - xMin || 1;
+    const scaleX = (val) => (val - xMin) / xRange * width;
+    const scaleY = (val) => height - val * height;
+    ctx.clearRect(0, 0, width, height);
+    let showCi = false;
+    if (showLoess && diagnostic.loess) {
+      const { loess } = diagnostic;
+      const firstProbePos = probes.positions[0];
+      const lastProbePos = probes.positions[probes.positions.length - 1];
+      showCi = probes.positions.length >= minProbesForCi;
+      for (const [fitted, ciLower, ciUpper, color] of [
+        [loess.group1_fitted, loess.group1_ci_lower, loess.group1_ci_upper, colors.group1],
+        [loess.group2_fitted, loess.group2_ci_lower, loess.group2_ci_upper, colors.group2]
+      ]) {
+        if (!fitted.length) continue;
+        const lPos = loess.positions;
+        let iStart = 0;
+        let iEnd = lPos.length - 1;
+        while (iStart < lPos.length && lPos[iStart] < firstProbePos) iStart++;
+        while (iEnd >= 0 && lPos[iEnd] > lastProbePos) iEnd--;
+        if (iStart > iEnd) continue;
+        if (showCi) {
+          ctx.globalAlpha = 0.12;
+          ctx.fillStyle = color;
+          ctx.beginPath();
+          for (let i = iStart; i <= iEnd; i++) {
+            ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciUpper[i]))));
+          }
+          for (let i = iEnd; i >= iStart; i--) {
+            ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciLower[i]))));
+          }
+          ctx.closePath();
+          ctx.fill();
+        }
+        ctx.globalAlpha = 0.8;
+        ctx.strokeStyle = color;
+        ctx.lineWidth = 2;
+        ctx.setLineDash(showCi ? [] : [6, 4]);
+        ctx.beginPath();
+        for (let i = iStart; i <= iEnd; i++) {
+          ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, fitted[i]))));
+        }
+        ctx.stroke();
+        ctx.setLineDash([]);
+      }
+    }
+    if (!showDots) {
+      ctx.globalAlpha = 1;
+      return { img: { minv: 0, maxv: 1, src: canvas.toDataURL("image/png") }, showCi };
+    }
+    for (let i = 0; i < probes.positions.length; i++) {
+      const x = scaleX(probes.positions[i]);
+      const isSig = probes.fdr[i] < fdr_cutoff;
+      const alpha = isSig ? 0.85 : 0.3;
+      ctx.globalAlpha = alpha;
+      ctx.fillStyle = colors.group1;
+      const m1 = probes.mean_group1[i];
+      if (m1 != null) {
+        ctx.beginPath();
+        ctx.arc(x, scaleY(m1), 4, 0, Math.PI * 2);
+        ctx.fill();
+      }
+      ctx.fillStyle = colors.group2;
+      const m2 = probes.mean_group2[i];
+      if (m2 != null) {
+        ctx.beginPath();
+        ctx.arc(x, scaleY(m2), 4, 0, Math.PI * 2);
+        ctx.fill();
+      }
+    }
+    ctx.globalAlpha = 1;
+    return { img: { minv: 0, maxv: 1, src: canvas.toDataURL("image/png") }, showCi };
+  }
+  makeDmrBedItems(dmrResult, settings) {
+    return dmrResult.dmrs.map((dmr) => {
+      const negLog = -Math.log10(Math.max(dmr.min_smoothed_fdr, 1e-300));
+      const alpha = Math.round(Math.min(255, Math.max(50, negLog / 10 * 255)));
+      const hex = alpha.toString(16).padStart(2, "0");
+      const base = dmr.direction === "hyper" ? settings.dmr.colors.hyper : settings.dmr.colors.hypo;
+      return { chr: dmr.chr, start: dmr.start, stop: dmr.stop, color: base + hex };
+    });
+  }
+  makeSigCpgBedItems(dmrResult, settings, chr, queryStart, queryStop) {
+    const diag = dmrResult.diagnostic;
+    if (!diag) return [];
+    const { probes } = diag;
+    const items = [];
+    const minDeltaBeta = 0.05;
+    for (let i = 0; i < probes.positions.length; i++) {
+      if (probes.fdr[i] >= settings.dmr.fdr_cutoff) continue;
+      const pos = probes.positions[i];
+      if (queryStart != null && queryStop != null && (pos < queryStart || pos > queryStop)) continue;
+      const mg1 = probes.mean_group1[i];
+      const mg2 = probes.mean_group2[i];
+      if (mg1 == null || mg2 == null) continue;
+      const deltaBeta = mg2 - mg1;
+      if (Math.abs(deltaBeta) < minDeltaBeta) continue;
+      const color = deltaBeta >= 0 ? settings.dmr.colors.hyper : settings.dmr.colors.hypo;
+      items.push({ chr, start: pos, stop: pos + 1, color });
+    }
+    return items;
+  }
+};
+
+export {
+  getDefaultDMRSettings,
+  CCRE_TRACK_NAME,
+  DmrViewModel
+};
+//# sourceMappingURL=chunk-VROF55EH.js.map

package/dist/chunk-VROF55EH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/dmr/settings/defaults.ts", "../plots/dmr/viewModel/DmrViewModel.ts"],
+  "sourcesContent": ["import type { DMRSettings } from './Settings.ts'\n\n// direction colours are shared with the server-rendered scan Manhattan\nexport { HYPER_COLOR, HYPO_COLOR } from '#shared/dmrColors.js'\nimport { HYPER_COLOR, HYPO_COLOR } from '#shared/dmrColors.js'\n\nexport function getDefaultDMRSettings(opts: any): DMRSettings {\n\tconst overrides = opts.settings || {}\n\t/* A dataset with no CpG-level matrix runs the region analysis on its element matrix, where one\n\trow is a cCRE, not a CpG. Those sit ~10kb apart against a CpG's ~100bp, so the CpG-scale window\n\tand kernel below would frame one element and smooth nothing. Scaled to element spacing instead.\n\tponytail: fixed values, not derived from the matrix's actual spacing \u2014 worth deriving only if a\n\tdataset shows up whose element density is far off this one's. The user can pan/zoom either way. */\n\tconst dm = opts?.app?.vocabApi?.termdbConfig?.queries?.dnaMethylation\n\t/* Per chromosome, not per dataset: a cohort with some shards built runs CpG resolution where one\n\texists and elements everywhere else (server resolveMethylationMatrix), so a dataset-wide flag gave\n\tthe fallback chromosomes a CpG-scale window over rows ~10 kb apart. cpgChroms is sent only for a\n\tshard-backed dataset without a genome-wide file. */\n\tconst chr = opts?.coordinateOverride?.chr\n\tconst elementScale =\n\t\tdm?.regionAnalysis == 'element' || (Array.isArray(dm?.cpgChroms) && !!chr && !dm.cpgChroms.includes(chr))\n\tconst defaults = {\n\t\tblockWidth: 800,\n\t\tpad: elementScale ? 100_000 : 2000,\n\t\tlambda: elementScale ? 50_000 : 1000,\n\t\tC: 2,\n\t\tfdr_cutoff: 0.05,\n\t\tcolors: {\n\t\t\tgroup1: '#3b5ee6',\n\t\t\tgroup2: '#c04e00',\n\t\t\thyper: HYPER_COLOR,\n\t\t\thypo: HYPO_COLOR\n\t\t},\n\t\tmaxLoessRegion: 250_000,\n\t\tminProbesForCi: 10,\n\t\tbackend: 'rust' as const,\n\t\tmaxRegionSize: 5_000_000\n\t}\n\n\t// Deep-merge colors so hyper/hypo defaults are preserved\n\t// when only group colors are overridden\n\tif (overrides.colors) {\n\t\tObject.assign(defaults.colors, overrides.colors)\n\t\tdelete overrides.colors\n\t}\n\n\treturn Object.assign(defaults, overrides)\n}\n", "import { first_genetrack_tolist } from '#common/1stGenetk'\n\n/** Name of the regulatory-element track in the genome config, if it declares one. */\nexport const CCRE_TRACK_NAME = 'ENCODE cCREs'\nimport type { TermdbDmrSuccessResponse, DmrDiagnostic } from '#types'\nimport type { DmrConfig, BedItem, LegendRow, DmrViewData } from '../DmrTypes.ts'\n\nexport class DmrViewModel {\n\tviewData: DmrViewData\n\n\tconstructor(\n\t\tdmrResult: TermdbDmrSuccessResponse,\n\t\tconfig: DmrConfig,\n\t\tgenomeObj: any,\n\t\tqueryChr: string,\n\t\tqueryStart?: number,\n\t\tqueryStop?: number\n\t) {\n\t\tconst { settings } = config\n\t\tconst dmrBedItems = this.makeDmrBedItems(dmrResult, settings)\n\t\tconst sigCpgBedItems = this.makeSigCpgBedItems(dmrResult, settings, queryChr, queryStart, queryStop)\n\n\t\tconst xRange = (queryStop ?? 0) - (queryStart ?? 0)\n\t\tconst loess = dmrResult.diagnostic?.loess\n\t\tconst showLoess = !!(loess && loess.group1_fitted.length > 0 && loess.group2_fitted.length > 0)\n\t\tconst showDots = xRange <= settings.dmr.maxLoessRegion\n\n\t\tconst betaTrackResult = dmrResult.diagnostic\n\t\t\t? this.renderBetaTrack(\n\t\t\t\t\tdmrResult.diagnostic,\n\t\t\t\t\tconfig,\n\t\t\t\t\tsettings.dmr.blockWidth,\n\t\t\t\t\tshowLoess,\n\t\t\t\t\tshowDots,\n\t\t\t\t\tqueryStart,\n\t\t\t\t\tqueryStop\n\t\t\t  )\n\t\t\t: undefined\n\n\t\tthis.viewData = {\n\t\t\ttklst: this.buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackResult?.img),\n\t\t\tlegendRows: this.buildLegendData(\n\t\t\t\tconfig,\n\t\t\t\tdmrResult.dmrs,\n\t\t\t\tsigCpgBedItems,\n\t\t\t\tshowLoess,\n\t\t\t\tshowDots,\n\t\t\t\tbetaTrackResult?.showCi ?? false\n\t\t\t),\n\t\t\tdiagnostic: dmrResult.diagnostic,\n\t\t\tdmrs: dmrResult.dmrs,\n\t\t\tdmrBedItems,\n\t\t\tshowLoess,\n\t\t\tshowDots\n\t\t}\n\t}\n\n\tprivate buildTrackList(\n\t\tdmrBedItems: BedItem[],\n\t\tsigCpgBedItems: BedItem[],\n\t\tgenomeObj: any,\n\t\tbetaTrackImg?: { minv: number; maxv: number; src: string }\n\t): any[] {\n\t\tconst tklst: any[] = []\n\t\tfirst_genetrack_tolist(genomeObj, tklst)\n\t\t/* Regulatory context, switched on here rather than left in the Tracks menu. A DMR next to a\n\t\tgene model says where it is; a DMR next to the cCREs says what it is sitting on, which is the\n\t\tquestion the element-level view was answering. Taken from the genome's own declaration by\n\t\tname, so a genome that does not declare it simply renders without the row. */\n\t\tconst ccre = (genomeObj?.tracks || []).find((t: any) => t.name == CCRE_TRACK_NAME)\n\t\tif (ccre) tklst.push(structuredClone(ccre))\n\t\ttklst.push({ type: 'bedj', name: 'DMRs', bedItems: dmrBedItems })\n\t\ttklst.push({ type: 'bedj', name: 'Sig. CpGs', bedItems: sigCpgBedItems })\n\t\tif (betaTrackImg) {\n\t\t\ttklst.push({\n\t\t\t\ttype: 'bigwig',\n\t\t\t\tname: 'Per-CpG Means',\n\t\t\t\theight: 150,\n\t\t\t\timgData: betaTrackImg\n\t\t\t})\n\t\t}\n\t\treturn tklst\n\t}\n\n\tprivate buildLegendData(\n\t\tconfig: DmrConfig,\n\t\tdmrs: TermdbDmrSuccessResponse['dmrs'],\n\t\tsigCpgBedItems: BedItem[],\n\t\tshowLoess: boolean,\n\t\tshowDots: boolean,\n\t\tshowCi: boolean\n\t): LegendRow[] {\n\t\tconst { colors } = config.settings.dmr\n\t\tconst g1 = config.group1Name || 'Group 1'\n\t\tconst g2 = config.group2Name || 'Group 2'\n\t\tconst meansItems: LegendRow['items'] = []\n\t\tif (showDots) {\n\t\t\tmeansItems.push({ text: `${g1} (control)`, color: colors.group1 }, { text: `${g2} (case)`, color: colors.group2 })\n\t\t}\n\t\tif (showLoess) {\n\t\t\tconst ciLabel = showCi ? ' + 95% CI' : ''\n\t\t\tmeansItems.push(\n\t\t\t\t{ text: `${g1} LOESS trend${ciLabel}`, color: colors.group1, style: showCi ? 'shaded' : 'dashed' },\n\t\t\t\t{ text: `${g2} LOESS trend${ciLabel}`, color: colors.group2, style: showCi ? 'shaded' : 'dashed' }\n\t\t\t)\n\t\t}\n\t\tconst rows: LegendRow[] = [{ label: 'Per-CpG Means', items: meansItems }]\n\t\t// Only show DMR legend entries for directions present in the results\n\t\tconst hasHyper = dmrs.some(d => d.direction === 'hyper')\n\t\tconst hasHypo = dmrs.some(d => d.direction === 'hypo')\n\t\tif (hasHyper || hasHypo) {\n\t\t\tconst items: LegendRow['items'] = []\n\t\t\tif (hasHyper) items.push({ text: 'Hypermethylated', color: colors.hyper })\n\t\t\tif (hasHypo) items.push({ text: 'Hypomethylated', color: colors.hypo })\n\t\t\trows.push({ label: 'DMR', items })\n\t\t}\n\t\tif (sigCpgBedItems.length) {\n\t\t\tconst items: LegendRow['items'] = []\n\t\t\tconst hasHyperCpg = sigCpgBedItems.some(b => b.color === colors.hyper)\n\t\t\tconst hasHypoCpg = sigCpgBedItems.some(b => b.color === colors.hypo)\n\t\t\tif (hasHyperCpg) items.push({ text: 'Hyper (FDR sig.)', color: colors.hyper })\n\t\t\tif (hasHypoCpg) items.push({ text: 'Hypo (FDR sig.)', color: colors.hypo })\n\t\t\trows.push({ label: 'Sig. CpGs', items })\n\t\t}\n\t\treturn rows\n\t}\n\n\t/**\n\t * Render the per-CpG means scatter plot to an offscreen canvas and return\n\t * a data URI suitable for the bigwig imgData track.\n\t */\n\tprivate renderBetaTrack(\n\t\tdiagnostic: DmrDiagnostic,\n\t\tconfig: DmrConfig,\n\t\tblockWidth: number,\n\t\tshowLoess: boolean,\n\t\tshowDots: boolean,\n\t\tqueryStart?: number,\n\t\tqueryStop?: number\n\t): { img: { minv: number; maxv: number; src: string }; showCi: boolean } | undefined {\n\t\tconst { probes } = diagnostic\n\t\tif (!probes.positions.length) return undefined\n\n\t\tconst { colors, fdr_cutoff, minProbesForCi } = config.settings.dmr\n\t\tconst dpr = typeof window !== 'undefined' && window.devicePixelRatio > 1 ? window.devicePixelRatio : 1\n\t\tconst width = blockWidth\n\t\tconst height = 150\n\n\t\tconst canvas = document.createElement('canvas')\n\t\tcanvas.width = width * dpr\n\t\tcanvas.height = height * dpr\n\t\tconst ctx = canvas.getContext('2d')\n\t\tif (!ctx) return undefined\n\t\tctx.scale(dpr, dpr)\n\n\t\t// Use the full block view range so dots align with bedj tracks above.\n\t\t// The block stretches the image to fill the view from queryStart to queryStop.\n\t\tconst xMin = queryStart ?? probes.positions[0]\n\t\tconst xMax = queryStop ?? probes.positions[probes.positions.length - 1]\n\t\tconst xRange = xMax - xMin || 1\n\t\tconst scaleX = (val: number) => ((val - xMin) / xRange) * width\n\t\tconst scaleY = (val: number) => height - val * height // beta 0-1\n\n\t\t// Transparent background so block mouse events (yellow line) show through\n\t\tctx.clearRect(0, 0, width, height)\n\n\t\t// DMR region shading omitted \u2014 already shown as a bedj track above\n\n\t\t// Draw LOESS curves with shaded CI regions, clipped to probe data range.\n\t\t// Only show CIs when there are enough probes for a reliable estimate.\n\t\tlet showCi = false\n\t\tif (showLoess && diagnostic.loess) {\n\t\t\tconst { loess } = diagnostic\n\t\t\tconst firstProbePos = probes.positions[0]\n\t\t\tconst lastProbePos = probes.positions[probes.positions.length - 1]\n\t\t\tshowCi = probes.positions.length >= minProbesForCi\n\n\t\t\tfor (const [fitted, ciLower, ciUpper, color] of [\n\t\t\t\t[loess.group1_fitted, loess.group1_ci_lower, loess.group1_ci_upper, colors.group1],\n\t\t\t\t[loess.group2_fitted, loess.group2_ci_lower, loess.group2_ci_upper, colors.group2]\n\t\t\t] as [number[], number[], number[], string][]) {\n\t\t\t\tif (!fitted.length) continue\n\t\t\t\tconst lPos = loess.positions\n\n\t\t\t\t// Find LOESS indices within the range of actual probe positions\n\t\t\t\tlet iStart = 0\n\t\t\t\tlet iEnd = lPos.length - 1\n\t\t\t\twhile (iStart < lPos.length && lPos[iStart] < firstProbePos) iStart++\n\t\t\t\twhile (iEnd >= 0 && lPos[iEnd] > lastProbePos) iEnd--\n\t\t\t\tif (iStart > iEnd) continue\n\n\t\t\t\tif (showCi) {\n\t\t\t\t\t// Draw CI as shaded region\n\t\t\t\t\tctx.globalAlpha = 0.12\n\t\t\t\t\tctx.fillStyle = color\n\t\t\t\t\tctx.beginPath()\n\t\t\t\t\tfor (let i = iStart; i <= iEnd; i++) {\n\t\t\t\t\t\tctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciUpper[i]))))\n\t\t\t\t\t}\n\t\t\t\t\tfor (let i = iEnd; i >= iStart; i--) {\n\t\t\t\t\t\tctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciLower[i]))))\n\t\t\t\t\t}\n\t\t\t\t\tctx.closePath()\n\t\t\t\t\tctx.fill()\n\t\t\t\t}\n\n\t\t\t\t// Draw LOESS fitted curve (dashed when no CI, solid otherwise)\n\t\t\t\tctx.globalAlpha = 0.8\n\t\t\t\tctx.strokeStyle = color\n\t\t\t\tctx.lineWidth = 2\n\t\t\t\tctx.setLineDash(showCi ? [] : [6, 4])\n\t\t\t\tctx.beginPath()\n\t\t\t\tfor (let i = iStart; i <= iEnd; i++) {\n\t\t\t\t\tctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, fitted[i]))))\n\t\t\t\t}\n\t\t\t\tctx.stroke()\n\t\t\t\tctx.setLineDash([])\n\t\t\t}\n\t\t}\n\n\t\t// Draw dots (hidden for large regions where only LOESS is shown)\n\t\tif (!showDots) {\n\t\t\tctx.globalAlpha = 1\n\t\t\treturn { img: { minv: 0, maxv: 1, src: canvas.toDataURL('image/png') }, showCi }\n\t\t}\n\t\tfor (let i = 0; i < probes.positions.length; i++) {\n\t\t\tconst x = scaleX(probes.positions[i])\n\t\t\tconst isSig = probes.fdr[i] < fdr_cutoff\n\t\t\tconst alpha = isSig ? 0.85 : 0.3\n\n\t\t\t// Group 1 (control)\n\t\t\tctx.globalAlpha = alpha\n\t\t\tctx.fillStyle = colors.group1\n\t\t\tconst m1 = probes.mean_group1[i]\n\t\t\tif (m1 != null) {\n\t\t\t\tctx.beginPath()\n\t\t\t\tctx.arc(x, scaleY(m1), 4, 0, Math.PI * 2)\n\t\t\t\tctx.fill()\n\t\t\t}\n\n\t\t\t// Group 2 (case)\n\t\t\tctx.fillStyle = colors.group2\n\t\t\tconst m2 = probes.mean_group2[i]\n\t\t\tif (m2 != null) {\n\t\t\t\tctx.beginPath()\n\t\t\t\tctx.arc(x, scaleY(m2), 4, 0, Math.PI * 2)\n\t\t\t\tctx.fill()\n\t\t\t}\n\t\t}\n\t\tctx.globalAlpha = 1\n\n\t\treturn { img: { minv: 0, maxv: 1, src: canvas.toDataURL('image/png') }, showCi }\n\t}\n\n\tprivate makeDmrBedItems(dmrResult: TermdbDmrSuccessResponse, settings: DmrConfig['settings']): BedItem[] {\n\t\treturn dmrResult.dmrs.map(dmr => {\n\t\t\t// Map -log10(min_smoothed_fdr) to alpha: more significant = more opaque\n\t\t\tconst negLog = -Math.log10(Math.max(dmr.min_smoothed_fdr, 1e-300))\n\t\t\tconst alpha = Math.round(Math.min(255, Math.max(50, (negLog / 10) * 255)))\n\t\t\tconst hex = alpha.toString(16).padStart(2, '0')\n\t\t\tconst base = dmr.direction === 'hyper' ? settings.dmr.colors.hyper : settings.dmr.colors.hypo\n\t\t\treturn { chr: dmr.chr, start: dmr.start, stop: dmr.stop, color: base + hex }\n\t\t})\n\t}\n\n\tprivate makeSigCpgBedItems(\n\t\tdmrResult: TermdbDmrSuccessResponse,\n\t\tsettings: DmrConfig['settings'],\n\t\tchr: string,\n\t\tqueryStart?: number,\n\t\tqueryStop?: number\n\t): BedItem[] {\n\t\tconst diag = dmrResult.diagnostic\n\t\tif (!diag) return []\n\t\tconst { probes } = diag\n\t\tconst items: BedItem[] = []\n\t\tconst minDeltaBeta = 0.05\n\t\tfor (let i = 0; i < probes.positions.length; i++) {\n\t\t\tif (probes.fdr[i] >= settings.dmr.fdr_cutoff) continue\n\t\t\tconst pos = probes.positions[i]\n\t\t\tif (queryStart != null && queryStop != null && (pos < queryStart || pos > queryStop)) continue\n\t\t\tconst mg1 = probes.mean_group1[i]\n\t\t\tconst mg2 = probes.mean_group2[i]\n\t\t\tif (mg1 == null || mg2 == null) continue\n\t\t\tconst deltaBeta = mg2 - mg1\n\t\t\tif (Math.abs(deltaBeta) < minDeltaBeta) continue\n\t\t\tconst color = deltaBeta >= 0 ? settings.dmr.colors.hyper : settings.dmr.colors.hypo\n\t\t\titems.push({ chr, start: pos, stop: pos + 1, color })\n\t\t}\n\t\treturn items\n\t}\n}\n"],
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+}