@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/DmrPlot-3R24PTXP.js

@@ -0,0 +1,640 @@
+import {
+  PlotBase,
+  first_genetrack_tolist,
+  sayerror,
+  table2col
+} from "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import {
+  dofetch3,
+  formatElapsedTime
+} from "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.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-2MABX5QO.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-3R24PTXP.js.map