@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/DmrPlot-QKUX5XUW.js

@@ -1,637 +0,0 @@
-import {
-  PlotBase,
-  first_genetrack_tolist,
-  sayerror,
-  table2col
-} from "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3,
-  formatElapsedTime
-} from "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/dmr/settings/defaults.ts
-function getDefaultDMRSettings(opts) {
-  const overrides = opts.settings || {};
-  const defaults = {
-    blockWidth: 800,
-    pad: 2e3,
-    lambda: 1e3,
-    C: 2,
-    fdr_cutoff: 0.05,
-    colors: {
-      group1: "#3b5ee6",
-      group2: "#c04e00",
-      hyper: "#e66101",
-      hypo: "#5e81f4"
-    },
-    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/model/DmrModel.ts
-var DmrModel = class {
-  constructor(config, vocab) {
-    this.config = config;
-    this.vocab = vocab;
-  }
-  async fetchDmr(chr, start, stop, signal) {
-    const { group1, group2, settings } = this.config;
-    const { genome, dslabel } = this.vocab;
-    return dofetch3("termdb/dmr", {
-      signal,
-      body: {
-        genome,
-        dslabel,
-        chr,
-        start,
-        stop,
-        group1,
-        group2,
-        lambda: settings.dmr.lambda,
-        C: settings.dmr.C,
-        fdr_cutoff: settings.dmr.fdr_cutoff,
-        group1Name: this.config.group1Name,
-        group2Name: this.config.group2Name,
-        blockWidth: settings.dmr.blockWidth,
-        devicePixelRatio: typeof window !== "undefined" ? window.devicePixelRatio : 1,
-        maxLoessRegion: settings.dmr.maxLoessRegion,
-        colors: settings.dmr.colors,
-        backend: settings.dmr.backend
-      }
-    });
-  }
-};
-
-// plots/dmr/viewModel/DmrViewModel.ts
-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);
-    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;
-  }
-};
-
-// plots/dmr/view/DmrView.ts
-var DmrView = class {
-  constructor(dom) {
-    this.dom = dom;
-  }
-  async renderBlock(viewData, genomeObj, settings, chr, start, stop, onCoordinateChange) {
-    const { Block } = await import("./block-L53P4UGQ.js");
-    return new Block({
-      holder: this.dom.holder,
-      genome: genomeObj,
-      chr,
-      start,
-      stop,
-      tklst: viewData.tklst,
-      nobox: true,
-      width: settings.blockWidth,
-      onCoordinateChange
-    });
-  }
-  updateTracks(viewData, blockInstance) {
-    for (const tk of blockInstance.tklst) {
-      const updated = viewData.tklst.find((t) => t.name === tk.name);
-      if (!updated) continue;
-      if (tk.type === "bedj" && updated.bedItems) {
-        tk.bedItems = updated.bedItems;
-        blockInstance.tk_load(tk);
-      } else if (tk.type === "bigwig" && updated.imgData) {
-        tk.imgData = updated.imgData;
-        blockInstance.tk_load(tk);
-      }
-    }
-  }
-  updateLegend(blockInstance, legendRows) {
-    if (!blockInstance?.legend?.holder) return;
-    const labels = ["Per-CpG Means", "DMR", "Sig. CpGs"];
-    blockInstance.legend.holder.selectAll("tr").filter((_d, i, nodes) => {
-      const td = nodes[i].querySelector("td");
-      return td && labels.includes(td.textContent);
-    }).remove();
-    this.renderLegend(blockInstance, legendRows);
-  }
-  renderLegend(blockInstance, legendRows) {
-    if (!blockInstance?.legend?.holder) return;
-    const { legendcolor, vpad } = blockInstance.legend;
-    for (const row of legendRows) {
-      const tr = blockInstance.legend.holder.append("tr");
-      tr.append("td").text(row.label).attr("style", `padding-right:10px;text-align:right;color:#555;border-right:solid 1px ${legendcolor}`);
-      const td = tr.append("td");
-      for (const entry of row.items) {
-        const item = td.append("div").attr("style", `display:inline-block;white-space:nowrap;padding:${vpad} 20px ${vpad} 0`);
-        if (entry.style === "shaded") {
-          item.append("div").attr(
-            "style",
-            `display:inline-block;width:18px;height:10px;background:${entry.color}20;border-top:2px solid ${entry.color};margin-right:5px;vertical-align:middle;border-radius:1px`
-          );
-        } else if (entry.style === "dashed") {
-          item.append("div").attr(
-            "style",
-            `display:inline-block;width:18px;height:0;border-top:2px dashed ${entry.color};margin-right:5px;vertical-align:middle`
-          );
-        } else {
-          item.append("div").attr(
-            "style",
-            `display:inline-block;width:12px;height:12px;background:${entry.color};margin-right:5px;border-radius:2px;vertical-align:middle`
-          );
-        }
-        item.append("div").attr("style", "display:inline-block;color:#555;font-size:.8em").text(entry.text);
-      }
-    }
-  }
-  renderDiagnostics(diagnostic, dmrs, fdr_cutoff) {
-    const panel = this.dom.diagnosticPanel;
-    panel.selectAll("*").remove();
-    panel.style("display", "block");
-    const { probes } = diagnostic;
-    const toggle = panel.append("div").attr("style", "cursor:default;font-size:12px;color:#888;padding:2px 0");
-    const statsContent = panel.append("div").style("display", "none");
-    let expanded = false;
-    toggle.text("+ Diagnostic details").on("click", () => {
-      expanded = !expanded;
-      toggle.text((expanded ? "\u2212 " : "+ ") + "Diagnostic details");
-      statsContent.style("display", expanded ? "block" : "none");
-    });
-    const spacings = diagnostic.probe_spacings;
-    const medianSpacing = spacings.length ? spacings.slice().sort((a, b) => a - b)[Math.floor(spacings.length / 2)] : 0;
-    const maxGap = spacings.length ? Math.max(...spacings) : 0;
-    const gapsOver1kb = spacings.filter((s) => s > 1e3).length;
-    const density = probes.positions.length > 1 ? probes.positions.length / ((probes.positions[probes.positions.length - 1] - probes.positions[0]) / 1e3) : 0;
-    const sigFdrCount = probes.fdr.filter((f) => f < fdr_cutoff).length;
-    const minDeltaBeta = 0.05;
-    const sigDualCount = probes.fdr.filter((f, i) => {
-      if (f >= fdr_cutoff) return false;
-      const m1 = probes.mean_group1[i];
-      const m2 = probes.mean_group2[i];
-      if (m1 == null || m2 == null) return false;
-      return Math.abs(m2 - m1) >= minDeltaBeta;
-    }).length;
-    const t = table2col({ holder: statsContent, disableScroll: true });
-    for (const [k, v] of [
-      ["Probes in region", String(probes.positions.length)],
-      ["FDR significant", `${sigFdrCount} (FDR < ${fdr_cutoff})`],
-      ["FDR + effect size", `${sigDualCount} (FDR < ${fdr_cutoff} & |\u0394\u03B2| \u2265 ${minDeltaBeta})`],
-      ["Probe density", `${density.toFixed(1)} probes/kb`],
-      ["Median spacing", `${medianSpacing.toFixed(0)} bp`],
-      ["Max gap", `${maxGap.toFixed(0)} bp`],
-      ["Gaps > 1kb", String(gapsOver1kb)],
-      ["DMRs called", String(dmrs.length)],
-      ...diagnostic.total_probes_analyzed ? [["Probes analyzed (genome-wide)", diagnostic.total_probes_analyzed.toLocaleString()]] : [],
-      ...diagnostic.elapsed_ms != null ? [["Analysis time", formatElapsedTime(diagnostic.elapsed_ms)]] : [],
-      ...diagnostic.peak_memory_mb != null ? [["Peak memory", `${diagnostic.peak_memory_mb.toFixed(1)} MB`]] : []
-    ]) {
-      t.addRow(k, v);
-    }
-  }
-  showOverlay() {
-    this.dom.loadingOverlay.style("display", "");
-  }
-  hideOverlay() {
-    this.dom.loadingOverlay.style("display", "none");
-  }
-  clearDiagnostics() {
-    this.dom.diagnosticPanel.selectAll("*").remove();
-    this.dom.diagnosticPanel.style("display", "none");
-  }
-  clearErrors() {
-    this.dom.error.selectAll("*").remove();
-  }
-  showLoessNote(show) {
-    this.dom.error.selectAll(".sjpp-loess-note").remove();
-    if (show) {
-      this.dom.error.append("div").attr("class", "sjpp-loess-note").style("color", "#888").style("font-size", ".8em").style("padding", "4px 0").text("Zoom in to see per-CpG dots.");
-    }
-  }
-};
-
-// plots/dmr/DmrPlot.ts
-var DmrPlot = class _DmrPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _DmrPlot.type;
-    this.blockInstance = null;
-    this.analyzedRegion = null;
-    const wrapper = opts.holder.append("div").style("position", "relative");
-    const loadingOverlay = wrapper.append("div").attr("class", "sjpp-spinner").style("display", "none").style("position", "absolute").style("z-index", "10").style("background-color", "rgba(255,255,255,0.65)");
-    const toggleDiv = opts.holder.append("div").style("padding", "2px 0");
-    const initBackend = opts.state?.config?.settings?.dmr?.backend || "rust";
-    const toggleBtn = toggleDiv.append("button").style("font-size", "11px").text(`Backend: ${initBackend === "rust" ? "Rust" : "R (DMRCate)"}`).on("click", () => {
-      const config = this.state.config;
-      const curr = config.settings.dmr.backend || "rust";
-      const next = curr === "rust" ? "r" : "rust";
-      toggleBtn.text(`Backend: ${next === "rust" ? "Rust" : "R (DMRCate)"}`);
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { settings: { dmr: { ...config.settings.dmr, backend: next } } }
-      });
-    });
-    this.dom = {
-      header: opts?.header,
-      holder: wrapper.append("div"),
-      loadingOverlay,
-      error: opts.holder.append("div"),
-      loading: opts.holder.append("div").text("Running DMR analysis\u2026"),
-      diagnosticPanel: opts.holder.append("div").style("display", "none")
-    };
-    this.view = new DmrView(this.dom);
-  }
-  static {
-    this.type = "dmr";
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw new Error(`No plot with id='${this.id}' found`);
-    return { config };
-  }
-  async init(appState) {
-    const { config } = this.getState(appState);
-    validateConfig(config);
-    if (this.dom.header) this.dom.header.text(config.headerText || "DMR Analysis");
-    this.genomeObj = this.app.opts.genome;
-    this.model = new DmrModel(config, this.app.vocabApi.vocab);
-    this.dom.loading.style("display", "block");
-    try {
-      const pad = config.settings.dmr.pad;
-      const chr = config.coordinateOverride.chr;
-      const start = Math.max(0, Number(config.coordinateOverride.start) - pad);
-      const stop = Number(config.coordinateOverride.stop) + pad;
-      checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
-      const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
-      if ("error" in dmrResult) {
-        sayerror(this.dom.error, dmrResult.error);
-        throw new Error(dmrResult.error);
-      }
-      this.analyzedRegion = { chr, start, stop };
-      const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop);
-      this.blockInstance = await this.view.renderBlock(
-        vm.viewData,
-        this.genomeObj,
-        config.settings.dmr,
-        chr,
-        start,
-        stop,
-        (rglst) => this.onBlockCoordinateChange(rglst)
-      );
-      this.view.renderLegend(this.blockInstance, vm.viewData.legendRows);
-      this.view.showLoessNote(!vm.viewData.showDots);
-      if (vm.viewData.diagnostic)
-        this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
-    } catch (e) {
-      if (this.app.isAbortError(e)) return;
-      const msg = e instanceof Error ? e.message : String(e);
-      sayerror(this.dom.error, msg);
-    }
-    this.dom.loading.style("display", "none");
-  }
-  async main() {
-    if (!this.analyzedRegion) return;
-    const config = this.state.config;
-    this.model = new DmrModel(config, this.app.vocabApi.vocab);
-    const c = config.coordinateOverride;
-    if (!c) return;
-    const pad = config.settings.dmr.pad;
-    const chr = c.chr;
-    const start = Math.max(0, Number(c.start) - pad);
-    const stop = Number(c.stop) + pad;
-    const a = this.analyzedRegion;
-    const coordsChanged = chr !== a.chr || start !== a.start || stop !== a.stop;
-    if (coordsChanged) {
-      this.view.showOverlay();
-      this.view.clearErrors();
-      try {
-        checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
-        const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
-        if ("error" in dmrResult) {
-          sayerror(this.dom.error, dmrResult.error);
-          throw new Error(dmrResult.error);
-        }
-        this.analyzedRegion = { chr, start, stop };
-        const blkRegion = this.blockInstance?.rglst?.[0];
-        const viewStart = blkRegion?.start ?? start;
-        const viewStop = blkRegion?.stop ?? stop;
-        const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, viewStart, viewStop);
-        this.view.updateTracks(vm.viewData, this.blockInstance);
-        this.view.updateLegend(this.blockInstance, vm.viewData.legendRows);
-        this.view.showLoessNote(!vm.viewData.showDots);
-        this.view.clearDiagnostics();
-        if (vm.viewData.diagnostic)
-          this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
-      } catch (e) {
-        if (this.app.isAbortError(e)) return;
-        const msg = e instanceof Error ? e.message : String(e);
-        sayerror(this.dom.error, msg);
-      }
-      this.view.hideOverlay();
-    } else {
-      this.dom.holder.selectAll("*").remove();
-      this.view.clearErrors();
-      this.dom.loading.style("display", "block");
-      this.blockInstance = null;
-      try {
-        checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
-        const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
-        if ("error" in dmrResult) {
-          sayerror(this.dom.error, dmrResult.error);
-          throw new Error(dmrResult.error);
-        }
-        this.analyzedRegion = { chr, start, stop };
-        const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop);
-        this.blockInstance = await this.view.renderBlock(
-          vm.viewData,
-          this.genomeObj,
-          config.settings.dmr,
-          chr,
-          start,
-          stop,
-          (rglst) => this.onBlockCoordinateChange(rglst)
-        );
-        this.view.renderLegend(this.blockInstance, vm.viewData.legendRows);
-        this.view.showLoessNote(!vm.viewData.showDots);
-        if (vm.viewData.diagnostic)
-          this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
-      } catch (e) {
-        if (this.app.isAbortError(e)) return;
-        const msg = e instanceof Error ? e.message : String(e);
-        sayerror(this.dom.error, msg);
-      }
-      this.dom.loading.style("display", "none");
-    }
-  }
-  onBlockCoordinateChange(rglst) {
-    if (!this.analyzedRegion || !rglst.length) return;
-    const r = rglst[0];
-    if (r.start >= r.stop || r.start < 0) return;
-    this.view.clearErrors();
-    const a = this.analyzedRegion;
-    if (r.chr === a.chr && r.start === a.start && r.stop === a.stop) return;
-    this.app.dispatch({
-      type: "plot_edit",
-      id: this.id,
-      config: { coordinateOverride: { chr: r.chr, start: r.start, stop: r.stop } }
-    });
-  }
-};
-var componentInit = getCompInit(DmrPlot);
-function getPlotConfig(opts) {
-  validateConfig(opts);
-  const config = {
-    settings: {
-      dmr: getDefaultDMRSettings(opts)
-    }
-  };
-  return copyMerge(config, opts);
-}
-function validateConfig(opts) {
-  if (!opts.coordinateOverride) throw new Error("coordinateOverride (chr/start/stop) is required for DMR plot");
-  if (!opts.group1) throw new Error("group1 is required for DMR plot");
-  if (!opts.group2) throw new Error("group2 is required for DMR plot");
-}
-function checkRegionSize(span, maxRegionSize) {
-  if (span > maxRegionSize) {
-    const mbLimit = (maxRegionSize / 1e6).toFixed(0);
-    const mbSpan = (span / 1e6).toFixed(1);
-    throw new Error(`Region too large for DMR analysis (${mbSpan} Mb). Maximum is ${mbLimit} Mb.`);
-  }
-}
-export {
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=DmrPlot-QKUX5XUW.js.map