@datagrok/proteomics 1.0.1 → 1.2.0

package/src/viewers/volcano.ts

@@ -0,0 +1,690 @@
+import * as DG from 'datagrok-api/dg';
+import * as ui from 'datagrok-api/ui';
+import * as rxjs from 'rxjs';
+import {debounceTime} from 'rxjs/operators';
+import {findColumn} from '../utils/column-detection';
+import {SEMTYPE, DIRECTION_COLORS_BASE, DEFAULT_FC_THRESHOLD,
+  DEFAULT_P_THRESHOLD} from '../utils/proteomics-types';
+import {parseAccession} from '../panels/uniprot-panel';
+import {getGroups, getOrganism} from '../analysis/experiment-setup';
+import {
+  getSubcellularLocations,
+  LOCATION_COLORS,
+  ProgressCb,
+} from '../analysis/subcellular-location';
+
+/** -log10 of the smallest representable positive double, used as a sentinel for
+ * p-values that underflow to literal 0 (e.g. from t-test extreme inputs).
+ * Plotting at this height keeps the point visible but clearly off-scale,
+ * rather than colliding with real values like p = 1e-10. */
+const UNDERFLOW_NEGLOG10 = -Math.log10(Number.MIN_VALUE);
+
+/** Significance metric the volcano Y axis / classification is computed from. */
+export type MetricKind = 'adj.p-value' | 'p-value';
+
+/** Active color dimension on the volcano (significance categories vs subcellular location). */
+export type ColorDim = 'significance' | 'location';
+
+/** Stable, generic column names. The Y/color bindings keep these names across
+ * a metric/color toggle; only the values change in place (Pitfall 5 — never
+ * early-return on existence, never remove+re-add a bound column). */
+const NEG_LOG_COL = 'negLog10P';
+const DIRECTION_COL = 'direction';
+export const LOCATION_COL = 'Subcellular Location';
+
+/** Persists the active metric on the DataFrame so the Volcano Options dialog
+ * (G2) and the axis-label overlay (G1) can derive Y-axis text without
+ * re-reading scatter props. recomputeVolcano updates this on every toggle. */
+export const VOLCANO_METRIC_TAG = 'proteomics.volcano_metric';
+
+/** Module-level subscription store mirrors `enrichment-viewers.ts:9` —
+ * disposed at the start of every createVolcanoPlot to prevent stacked
+ * overlays / frozen counters on viewer re-entry (Pitfall 6). */
+let activeVolcanoSubscriptions: rxjs.Subscription[] = [];
+
+/** Marker class on a volcano's scatter root; scopes the axis-chip-hiding
+ * stylesheet so it only affects our volcanoes, never other scatterplots. */
+const VOLCANO_ROOT_CLASS = 'proteomics-volcano';
+
+/** Injects the scoped stylesheet that hides the platform's X/Y axis
+ * column-selector chips inside a volcano (they duplicated our custom axis
+ * labels). `.d4-vertical` (Y) and `.d4-bottom-center` (X) only — the color
+ * (`.d4-vertical-right`) and size selectors stay. Idempotent: injected once. */
+function ensureVolcanoStyles(): void {
+  const id = 'proteomics-volcano-styles';
+  if (document.getElementById(id)) return;
+  const style = document.createElement('style');
+  style.id = id;
+  style.textContent =
+    `.${VOLCANO_ROOT_CLASS} .d4-column-selector.d4-vertical,` +
+    `.${VOLCANO_ROOT_CLASS} .d4-column-selector.d4-bottom-center{display:none !important;}`;
+  document.head.appendChild(style);
+}
+
+/** Resolves the significance column for the requested metric. `p-value` falls
+ * back to `adj.p-value` when the raw p-value column is absent (D-06 guard — no
+ * throw, stays on adj.p-value). Throws only when adj.p-value itself is missing
+ * (genuinely no DE result). */
+function pickMetricColumn(df: DG.DataFrame, metric: MetricKind): DG.Column {
+  if (metric === 'p-value') {
+    const p = df.col('p-value');
+    if (p) return p;
+  }
+  const adj = df.col('adj.p-value');
+  if (!adj)
+    throw new Error('adj.p-value column not found');
+  return adj;
+}
+
+/** Ensures the -log10(metric) column exists and reflects `metric`. The column
+ * name is FIXED so the scatter Y binding is stable; values are ALWAYS re-init
+ * in place so a metric toggle updates the axis without rebinding. */
+export function ensureNegLog10Column(
+  df: DG.DataFrame, metric: MetricKind = 'adj.p-value',
+): string {
+  const pCol = pickMetricColumn(df, metric);
+  const col = df.col(NEG_LOG_COL) ?? df.columns.addNewFloat(NEG_LOG_COL);
+  col.init((i) => {
+    if (pCol.isNone(i)) return DG.FLOAT_NULL;
+    const p = pCol.get(i) as number;
+    return p > 0 ? -Math.log10(p) : UNDERFLOW_NEGLOG10;
+  });
+  return NEG_LOG_COL;
+}
+
+/** LOCKED color contract (D-04, CONTEXT.md §"Specifics"): magenta = numerator
+ * (group1), cyan = denominator (group2), gray = NS. Keys are derived per call
+ * from `getGroups(df)`; the ARGB ints are the invariant base, now sourced from
+ * `proteomics-types` and re-exported here for existing importers. */
+export {DIRECTION_COLORS_BASE};
+
+/** Ensures the direction column, classified against the chosen `metric` (same
+ * column the Y axis uses, so dots and coloring never disagree). Updated in
+ * place — never remove+re-add (preserves viewer/grid bindings). D-04 migration:
+ * category strings derive from `getGroups(df)` (`Enriched in {g1}` / `Enriched
+ * in {g2}` / `Not significant`), color map is the LOCKED magenta/cyan/gray. */
+export function ensureDirectionColumn(
+  df: DG.DataFrame,
+  fcThreshold: number,
+  pThreshold: number,
+  metric: MetricKind = 'adj.p-value',
+): string {
+  const fcCol = df.col('log2FC');
+  if (!fcCol)
+    throw new Error('log2FC column not found');
+  const pCol = pickMetricColumn(df, metric);
+
+  const groups = getGroups(df);
+  const g1Label = groups ? `Enriched in ${groups.group1.name}` : 'Enriched in group1';
+  const g2Label = groups ? `Enriched in ${groups.group2.name}` : 'Enriched in group2';
+  const nsLabel = 'Not significant';
+
+  const n = df.rowCount;
+  const vals: string[] = new Array(n);
+  for (let i = 0; i < n; i++) {
+    if (fcCol.isNone(i) || pCol.isNone(i)) { vals[i] = nsLabel; continue; }
+    const fc = fcCol.get(i) as number;
+    const p = pCol.get(i) as number;
+    if (p <= pThreshold && fc > fcThreshold) vals[i] = g1Label;
+    else if (p <= pThreshold && fc < -fcThreshold) vals[i] = g2Label;
+    else vals[i] = nsLabel;
+  }
+
+  const col = df.col(DIRECTION_COL) ?? df.columns.addNewString(DIRECTION_COL);
+  col.init((i) => vals[i]);
+  col.meta.colors.setCategorical({
+    [g1Label]: DIRECTION_COLORS_BASE.enrichedG1,
+    [g2Label]: DIRECTION_COLORS_BASE.enrichedG2,
+    [nsLabel]: DIRECTION_COLORS_BASE.notSig,
+  });
+  return DIRECTION_COL;
+}
+
+/** FNV-1a 32-bit hex hash. Deterministic, dependency-free, fast enough for the
+ * ~8k-accession stable-sorted join that ensureLocationColumn feeds it. Used
+ * only as a cache-invalidation key on the Subcellular Location column. */
+function fnv1aHex(s: string): string {
+  let h = 0x811c9dc5;
+  for (let i = 0; i < s.length; i++) {
+    h ^= s.charCodeAt(i);
+    h = (h + ((h << 1) + (h << 4) + (h << 7) + (h << 8) + (h << 24))) >>> 0;
+  }
+  return h.toString(16).padStart(8, '0');
+}
+
+/** Cache-invalidation key on the Subcellular Location COLUMN (not the
+ * DataFrame). This is the first column-level tag in the package — the
+ * DataFrame tag convention covers whole-pipeline workflow state, while
+ * per-column cache-invalidation metadata belongs on the column. Documented
+ * in 13-08 SUMMARY.md as a new convention. */
+const LOCATION_HASH_TAG = 'proteomics.location_acc_hash';
+
+/** Ensures the 'Subcellular Location' categorical column using the shared
+ * verbatim-CK-omics service (13-04). Bulk-init string column, the LOCKED 11+1
+ * palette via setCategorical, semType = SUBCELLULAR_LOCATION. In place.
+ *
+ * Short-circuits when the column already exists AND its accession-set hash
+ * tag matches the current accession set — skipping the entire fetch+init
+ * pipeline. The palette and semType survive on the column object across
+ * the short-circuit because `col.meta.colors.setCategorical` and
+ * `col.semType` are set on the same column object as last run.
+ *
+ * `progress` is forwarded to getSubcellularLocations for the fetch phases
+ * AND fired once for the 'init-column' phase so the dialog's pi can advance
+ * past the post-fetch bulk-init. */
+export async function ensureLocationColumn(
+  df: DG.DataFrame, progress?: ProgressCb,
+): Promise<string> {
+  const idCol = findColumn(df, SEMTYPE.PROTEIN_ID,
+    ['primary protein id', 'protein id', 'protein ids', 'accession', 'uniprot']) ??
+    df.col('Primary Protein ID') ?? df.col('Protein ID');
+
+  const n = df.rowCount;
+  const accForRow: (string | null)[] = new Array(n).fill(null);
+  const accessions = new Set<string>();
+  if (idCol) {
+    for (let i = 0; i < n; i++) {
+      const raw = idCol.get(i) as string | null;
+      const acc = raw ? parseAccession(raw) : null;
+      accForRow[i] = acc;
+      if (acc) accessions.add(acc);
+    }
+  }
+
+  // Stable-sorted join → deterministic across calls regardless of row order.
+  const currentHash = fnv1aHex([...accessions].sort().join('|'));
+
+  const existing = df.col(LOCATION_COL);
+  if (existing && existing.getTag(LOCATION_HASH_TAG) === currentHash) {
+    // Short-circuit: column already populated for this exact accession set.
+    // Fire 'init-column' so the dialog's pi can advance to 100% and close
+    // cleanly without sitting at 0%.
+    progress?.(1, 1, 'init-column');
+    return LOCATION_COL;
+  }
+
+  // Organism (set by the enrichment dialog, persisted as a df tag) narrows the
+  // gene-fallback pass so non-human data isn't mis-colored from human entries.
+  const locByAcc = await getSubcellularLocations(
+    [...accessions], getOrganism(df), progress);
+  const vals: string[] = new Array(n);
+  for (let i = 0; i < n; i++) {
+    const acc = accForRow[i];
+    vals[i] = (acc && locByAcc.get(acc)) || 'Unknown';
+  }
+
+  const col = existing ?? df.columns.addNewString(LOCATION_COL);
+  col.init((i) => vals[i]);
+  col.meta.colors.setCategorical(LOCATION_COLORS);
+  col.semType = SEMTYPE.SUBCELLULAR_LOCATION;
+  // Column-level cache-invalidation tag — see plan 13-08 patterns-established.
+  col.setTag(LOCATION_HASH_TAG, currentHash);
+  // Final progress tick after bulk-init so the dialog's pi advances past
+  // the network phase into 'init-column' done.
+  progress?.(1, 1, 'init-column');
+  return LOCATION_COL;
+}
+
+/** Replaces (never stacks) the volcano threshold lines: horizontal at the
+ * significance cutoff and the ±fold-change verticals. */
+function applyThresholdLines(
+  df: DG.DataFrame, yColName: string, fcThreshold: number, pThreshold: number,
+): void {
+  const hLine = -Math.log10(pThreshold);
+  const yFormulaPrefix = `\${${yColName}}`;
+  const fcFormulaPrefix = `\${log2FC}`;
+  df.meta.formulaLines.items = df.meta.formulaLines.items.filter((line) => {
+    const f = line.formula ?? '';
+    return !(typeof f === 'string' &&
+      (f.startsWith(yFormulaPrefix) || f.startsWith(fcFormulaPrefix)));
+  });
+  df.meta.formulaLines.addLine(
+    {formula: `${yFormulaPrefix} = ${hLine}`, color: '#888888', width: 1, visible: true});
+  df.meta.formulaLines.addLine(
+    {formula: `${fcFormulaPrefix} = ${fcThreshold}`, color: '#888888', width: 1, visible: true});
+  df.meta.formulaLines.addLine(
+    {formula: `${fcFormulaPrefix} = ${-fcThreshold}`, color: '#888888', width: 1, visible: true});
+}
+
+/** UI-SPEC §"Copywriting": Y-axis label depends on the active metric;
+ * defaults to adj.p-value mode when the tag is absent. */
+function yAxisLabelForMetric(metric: MetricKind | null | undefined): string {
+  return metric === 'p-value' ? '-Log10(p-value)' : '-Log10(Q-value)';
+}
+
+/** G2 dialog-preload contract: every input in the Volcano Options dialog is
+ * seeded from {@link readVolcanoState}. Source-of-truth precedence:
+ *   1. `sp.getOptions().look.colorColumnName` → colorDim
+ *   2. `df.tag(VOLCANO_METRIC_TAG)` → metric (set by recomputeVolcano)
+ * Pitfall 2 — the dialog snapshots at open time; OK uses input values, never
+ * a re-read of sp.getOptions. */
+export interface VolcanoState {
+  metric: MetricKind;
+  colorDim: ColorDim;
+}
+
+export function readVolcanoState(df: DG.DataFrame, sp: DG.ScatterPlotViewer): VolcanoState {
+  const opts = sp.getOptions() as any;
+  const look = opts?.look ?? {};
+  const colorDim: ColorDim = look.colorColumnName === LOCATION_COL ? 'location' : 'significance';
+  const metric = (df.getTag(VOLCANO_METRIC_TAG) as MetricKind | null) ?? 'adj.p-value';
+  return {metric, colorDim};
+}
+
+/** Volcano title synthesis from `proteomics.groups` per UI-SPEC §"Copywriting":
+ * `Volcano Plot: {g1} vs {g2}`, or `Volcano Plot` when groups are unset. */
+function synthesizeVolcanoTitle(df: DG.DataFrame): string {
+  const groups = getGroups(df);
+  return groups ?
+    `Volcano Plot: ${groups.group1.name} vs ${groups.group2.name}` :
+    'Volcano Plot';
+}
+
+/** Disposes every subscription in `activeVolcanoSubscriptions` and removes any
+ * axis-label / counter overlays attached to `sp.root`. Called at the start of
+ * every createVolcanoPlot so re-entry never stacks DOM or strands subscribers
+ * pointing at a detached viewer (Pitfall 6). */
+function disposeVolcanoAttachments(sp?: DG.ScatterPlotViewer): void {
+  for (const s of activeVolcanoSubscriptions) s.unsubscribe();
+  activeVolcanoSubscriptions = [];
+  if (sp) {
+    for (const sel of [
+      '[data-volcano-axis-x]', '[data-volcano-axis-y]', '[data-volcano-counter]',
+      '[data-volcano-busy]',
+    ])
+      sp.root.querySelectorAll(sel).forEach((el) => el.remove());
+  }
+}
+
+/** Re-reads the Y-axis label DOM (if present) from the current metric tag.
+ * Called by recomputeVolcano after the tag is persisted so the label reflects
+ * the new metric immediately (sp.onPropertyChanged doesn't fire when only the
+ * tag changes — the yColumnName stays stable). */
+function refreshVolcanoAxisLabel(sp: DG.ScatterPlotViewer, df: DG.DataFrame): void {
+  const yLabel = sp.root.querySelector<HTMLElement>('[data-volcano-axis-y]');
+  if (yLabel) {
+    const metric = df.getTag(VOLCANO_METRIC_TAG) as MetricKind | null;
+    yLabel.textContent = yAxisLabelForMetric(metric);
+  }
+}
+
+/** D-06 live counter overlay: floating div anchored bottom-right of the
+ * volcano. Heading + Total + per-category counts (significance categories
+ * when color = direction, subcellular location categories when color =
+ * Subcellular Location). Counts iterate `df.filter` only (selection toggles
+ * trigger a recompute defensively but never change the displayed counts —
+ * CONTEXT D-06). Subscriptions are pushed into `activeVolcanoSubscriptions`
+ * so disposeVolcanoAttachments tears them down on re-entry (Pitfall 6). */
+function attachCounterOverlay(sp: DG.ScatterPlotViewer, df: DG.DataFrame): void {
+  const host = sp.root;
+  host.style.position = host.style.position || 'relative';
+
+  const overlay = ui.divV([]);
+  overlay.dataset.volcanoCounter = 'true';
+  Object.assign(overlay.style, {
+    position: 'absolute', bottom: '8px', right: '8px',
+    padding: '8px 16px', background: 'rgba(255,255,255,0.85)',
+    borderRadius: '4px', fontSize: '0.9em',
+    pointerEvents: 'none', zIndex: '5',
+  } as Partial<CSSStyleDeclaration>);
+  host.appendChild(overlay);
+
+  const recompute = (): void => {
+    const total = df.filter.trueCount;
+    const colorColName = sp.props.colorColumnName;
+    const colorCol = colorColName ? df.col(colorColName) : null;
+
+    // Iterate categories from the column's own category list so zero-count
+    // categories still render (D-06: empty filter still shows zeros, not
+    // just the categories present in the filtered subset).
+    const counts = new Map<string, number>();
+    let perCategoryEnabled = false;
+    if (colorCol && (colorColName === DIRECTION_COL || colorColName === LOCATION_COL)) {
+      perCategoryEnabled = true;
+      for (const cat of colorCol.categories) counts.set(cat, 0);
+      for (let i = 0; i < df.rowCount; i++) {
+        if (!df.filter.get(i)) continue;
+        if (colorCol.isNone(i)) continue;
+        const cat = colorCol.get(i) as string;
+        counts.set(cat, (counts.get(cat) ?? 0) + 1);
+      }
+    }
+
+    overlay.replaceChildren();
+    const heading = ui.divText('Visible Proteins');
+    heading.style.fontWeight = 'bold';
+    overlay.appendChild(heading);
+    overlay.appendChild(ui.divText(`Total: ${total.toLocaleString()}`));
+    if (perCategoryEnabled) {
+      for (const [cat, n] of counts)
+        overlay.appendChild(ui.divText(`${cat}: ${n.toLocaleString()}`));
+    }
+  };
+
+  recompute();
+  activeVolcanoSubscriptions.push(
+    df.onFilterChanged.pipe(debounceTime(50)).subscribe(recompute),
+    df.onSelectionChanged.pipe(debounceTime(50)).subscribe(recompute),
+    sp.onPropertyValueChanged.pipe(debounceTime(50)).subscribe(recompute),
+  );
+}
+
+/** Attaches DOM overlays for X and Y axis labels (the scatter has no
+ * xAxisCustomTitle / yAxisCustomTitle prop). X label is invariant; Y label is
+ * driven from VOLCANO_METRIC_TAG and re-rendered by refreshVolcanoAxisLabel. */
+function attachAxisLabels(sp: DG.ScatterPlotViewer, df: DG.DataFrame): void {
+  const host = sp.root;
+  host.style.position = host.style.position || 'relative';
+
+  const xLabel = ui.divText('Log2 Fold Change');
+  xLabel.dataset.volcanoAxisX = 'true';
+  Object.assign(xLabel.style, {
+    position: 'absolute', bottom: '4px', left: '50%',
+    transform: 'translateX(-50%)', fontSize: '0.85em',
+    pointerEvents: 'none', background: 'rgba(255,255,255,0.7)',
+    padding: '0 4px', zIndex: '4',
+  } as Partial<CSSStyleDeclaration>);
+  host.appendChild(xLabel);
+
+  const metric = df.getTag(VOLCANO_METRIC_TAG) as MetricKind | null;
+  const yLabel = ui.divText(yAxisLabelForMetric(metric));
+  yLabel.dataset.volcanoAxisY = 'true';
+  Object.assign(yLabel.style, {
+    position: 'absolute', left: '4px', top: '50%',
+    transform: 'translateY(-50%) rotate(-90deg)',
+    transformOrigin: 'left center', fontSize: '0.85em',
+    pointerEvents: 'none', background: 'rgba(255,255,255,0.7)',
+    padding: '0 4px', zIndex: '4',
+  } as Partial<CSSStyleDeclaration>);
+  host.appendChild(yLabel);
+
+  // Defensive: refresh on any property change as a secondary trigger
+  // (recomputeVolcano calls refreshVolcanoAxisLabel directly — this catches
+  // any external prop edit, e.g. user changes color column via property panel).
+  activeVolcanoSubscriptions.push(
+    sp.onPropertyValueChanged.pipe(debounceTime(50))
+      .subscribe(() => refreshVolcanoAxisLabel(sp, df)),
+  );
+}
+
+/** 13-10 in-volcano busy overlay. Centered card on `sp.root` showing a phase
+ * label and an optional detail line; updated per ProgressCb tick from the
+ * caller (e.g. volcanoOptions during a first-time subcellular-location fetch).
+ *
+ * The TaskBarProgressIndicator at the bottom of the platform shell is too easy
+ * to miss while the user stares at a stale-looking volcano (post-13-08 UAT
+ * Test 3). This overlay anchors progress on the surface the user is actually
+ * watching. Tagged with `data-volcano-busy` so disposeVolcanoAttachments
+ * sweeps it on createVolcanoPlot re-entry. */
+export function showVolcanoBusy(sp: DG.ScatterPlotViewer, label: string): void {
+  // Idempotent: replace any pre-existing overlay rather than stacking.
+  hideVolcanoBusy(sp);
+
+  const host = sp.root;
+  host.style.position = host.style.position || 'relative';
+
+  const overlay = ui.divV([]);
+  overlay.dataset.volcanoBusy = 'true';
+  Object.assign(overlay.style, {
+    position: 'absolute', top: '50%', left: '50%',
+    transform: 'translate(-50%, -50%)',
+    padding: '12px 20px', background: 'rgba(255,255,255,0.95)',
+    border: '1px solid #ccc', borderRadius: '6px',
+    boxShadow: '0 2px 8px rgba(0,0,0,0.15)',
+    fontSize: '0.95em', textAlign: 'center',
+    pointerEvents: 'none', zIndex: '6',
+    maxWidth: '320px',
+  } as Partial<CSSStyleDeclaration>);
+
+  const labelDiv = ui.divText(label);
+  labelDiv.style.fontWeight = 'bold';
+  labelDiv.style.marginBottom = '4px';
+  const detailDiv = ui.divText('');
+  detailDiv.style.fontSize = '0.85em';
+  detailDiv.style.color = '#666';
+  overlay.appendChild(labelDiv);
+  overlay.appendChild(detailDiv);
+  host.appendChild(overlay);
+}
+
+export function updateVolcanoBusy(
+  sp: DG.ScatterPlotViewer, label: string, detail?: string,
+): void {
+  const overlay = sp.root.querySelector<HTMLElement>('[data-volcano-busy]');
+  if (!overlay) return; // already torn down — caller raced detach
+  const [labelDiv, detailDiv] = Array.from(overlay.children) as HTMLElement[];
+  if (labelDiv) labelDiv.textContent = label;
+  if (detailDiv) detailDiv.textContent = detail ?? '';
+}
+
+export function hideVolcanoBusy(sp: DG.ScatterPlotViewer): void {
+  sp.root.querySelectorAll('[data-volcano-busy]').forEach((el) => el.remove());
+}
+
+/** Column that drives the volcano's point labels. Sparse: it holds the chosen
+ * display name only for the labeled rows and '' everywhere else. `~`-prefixed so
+ * it stays out of the grid. Labels bind to THIS column (showLabelsFor='All')
+ * instead of to df.selection, so labeling no longer hijacks the user's selection
+ * — that coupling surfaced as the confusing orange "N selected" on open and let
+ * the enrichment cross-link wipe the labels. */
+export const VOLCANO_LABEL_COL = '~Volcano label';
+/** Persisted top-N label count so the options dialog + search path can read it. */
+export const VOLCANO_TOPN_TAG = 'proteomics.volcano_top_n';
+
+/** Optional pinned axis maxima, stored as df tags so they survive the metric /
+ * color toggles that re-enter recomputeVolcano (tag-based state, like the metric
+ * and top-N). Empty = auto-scale. X is the symmetric |log2FC| bound (pins
+ * xMin=-xMax, xMax=+xMax); Y pins the −log10(p) maximum with yMin at 0. Lets
+ * analysts fix identical axes across contrasts for side-by-side comparison
+ * (CK x_max_var / y_max_var). */
+export const VOLCANO_XMAX_TAG = 'proteomics.volcano_x_max';
+export const VOLCANO_YMAX_TAG = 'proteomics.volcano_y_max';
+
+/** Reads the pinned axis maxima; a tag that is absent, non-numeric, or ≤ 0 reads
+ * as null (auto-scale). */
+export function getVolcanoAxisMax(df: DG.DataFrame): {xMax: number | null; yMax: number | null} {
+  const parse = (tag: string): number | null => {
+    const v = parseFloat(df.getTag(tag) ?? '');
+    return Number.isFinite(v) && v > 0 ? v : null;
+  };
+  return {xMax: parse(VOLCANO_XMAX_TAG), yMax: parse(VOLCANO_YMAX_TAG)};
+}
+
+/** Persists the pinned axis maxima; null / non-positive clears the tag (auto). */
+export function setVolcanoAxisMax(df: DG.DataFrame, xMax: number | null, yMax: number | null): void {
+  const write = (tag: string, v: number | null) =>
+    df.setTag(tag, v != null && Number.isFinite(v) && v > 0 ? String(v) : '');
+  write(VOLCANO_XMAX_TAG, xMax);
+  write(VOLCANO_YMAX_TAG, yMax);
+}
+
+/** Applies the pinned axis bounds from the df tags onto the scatterplot. When a
+ * bound is unset, resets that axis to the data's actual min/max (a fit-to-data
+ * reset) rather than NaN — the platform rejects a NaN viewport ("Viewport can't
+ * be infinite"). Called by createVolcanoPlot and every recomputeVolcano so a
+ * metric / color toggle keeps the pinned axes. */
+export function applyVolcanoAxisBounds(sp: DG.ScatterPlotViewer, df: DG.DataFrame): void {
+  const {xMax, yMax} = getVolcanoAxisMax(df);
+  if (xMax != null) {
+    sp.props.xMin = -xMax;
+    sp.props.xMax = xMax;
+  } else {
+    const fc = df.col('log2FC');
+    if (fc != null && Number.isFinite(fc.min) && Number.isFinite(fc.max)) {
+      const pad = Math.max((fc.max - fc.min) * 0.05, 1e-6);
+      sp.props.xMin = fc.min - pad;
+      sp.props.xMax = fc.max + pad;
+    }
+  }
+  if (yMax != null) {
+    sp.props.yMin = 0;
+    sp.props.yMax = yMax;
+  } else {
+    const y = df.col(NEG_LOG_COL);
+    if (y != null && Number.isFinite(y.max)) {
+      sp.props.yMin = 0;
+      sp.props.yMax = y.max * 1.05 + 1e-6;
+    }
+  }
+}
+
+/** Display Name (Plan 14-01) is canonical; Gene name is the pre-14-01 fallback. */
+function findLabelSource(df: DG.DataFrame): DG.Column | null {
+  return findColumn(df, SEMTYPE.DISPLAY_NAME, ['display name']) ??
+    findColumn(df, SEMTYPE.GENE_SYMBOL, ['gene name', 'gene symbol']);
+}
+
+/** Ranks filtered-in rows by significance (−log10p desc, |log2FC| desc) and
+ * returns the top-N row indices. Excludes FLOAT_NULL on either axis. */
+function topNBySignificance(df: DG.DataFrame, n: number): number[] {
+  if (n <= 0) return [];
+  const yCol = df.col(NEG_LOG_COL);
+  const fcCol = df.col('log2FC');
+  if (!yCol || !fcCol) return [];
+  const yRaw = yCol.getRawData() as Float32Array | Float64Array;
+  const fcRaw = fcCol.getRawData() as Float32Array | Float64Array;
+
+  const candidates: number[] = [];
+  for (let i = 0; i < df.rowCount; i++) {
+    if (!df.filter.get(i)) continue;
+    if (yRaw[i] === DG.FLOAT_NULL || fcRaw[i] === DG.FLOAT_NULL) continue;
+    candidates.push(i);
+  }
+  candidates.sort((a, b) => {
+    const dy = yRaw[b] - yRaw[a]; // higher -log10(p) first
+    if (dy !== 0) return dy;
+    return Math.abs(fcRaw[b]) - Math.abs(fcRaw[a]);
+  });
+  return candidates.slice(0, n);
+}
+
+/** Reads the persisted top-N label count (default 15). */
+export function getVolcanoTopN(df: DG.DataFrame): number {
+  const n = parseInt(df.getTag(VOLCANO_TOPN_TAG) ?? '', 10);
+  return Number.isFinite(n) && n >= 0 ? n : 15;
+}
+
+/** D-03 top-N point labels — decoupled from df.selection (Pitfall: selection-as-
+ * labels conflated the orange highlight with the label set and let the
+ * enrichment cross-link wipe it). Populates the sparse {@link VOLCANO_LABEL_COL}
+ * with the top-N proteins by significance (plus any `extraRows`, e.g. search
+ * matches), '' everywhere else, and binds it as the scatter's label source. The
+ * user's selection is never touched. `n=0` with no `extraRows` clears labels. */
+export function applyTopNLabels(
+  df: DG.DataFrame,
+  sp: DG.ScatterPlotViewer,
+  n: number = 15,
+  extraRows?: Iterable<number>,
+): void {
+  df.setTag(VOLCANO_TOPN_TAG, String(n));
+  const src = findLabelSource(df);
+  if (!src) return; // nothing to label with → don't add an empty technical column
+
+  // ensureFreshFloat-style idempotency: reuse the column if present, else add.
+  const labelCol = df.col(VOLCANO_LABEL_COL) ?? df.columns.addNewString(VOLCANO_LABEL_COL);
+
+  const show = new Set<number>(topNBySignificance(df, n));
+  if (extraRows) for (const i of extraRows) show.add(i);
+
+  // Bulk init (memory feedback_dg_column_bulk_init — never per-row set).
+  labelCol.init((i) => show.has(i) ? String(src.get(i) ?? '') : '');
+
+  sp.props.labelColumnNames = [VOLCANO_LABEL_COL];
+  sp.props.showLabelsFor = 'All';
+}
+
+/** Creates a volcano plot (ScatterPlotViewer). Defaults match the client
+ * CK-omics figure: metric = adj.p-value, color = significance (magenta/cyan/
+ * gray per D-04). G1 title is synthesized from `proteomics.groups`, D-03
+ * top-N labels are seeded into `df.selection`, label binding prefers
+ * `Display Name` (Plan 14-01 contract) with `Gene name` as a graceful fallback
+ * for DataFrames predating Plan 14-01. */
+export function createVolcanoPlot(
+  df: DG.DataFrame,
+  options?: {fcThreshold?: number; pThreshold?: number; topNLabels?: number; title?: string},
+): DG.ScatterPlotViewer {
+  const fcThreshold = options?.fcThreshold ?? DEFAULT_FC_THRESHOLD;
+  const pThreshold = options?.pThreshold ?? DEFAULT_P_THRESHOLD;
+
+  // Re-entry contract — dispose every overlay / subscription from a prior
+  // createVolcanoPlot call BEFORE attaching new ones (Pitfall 6). We do this
+  // again AFTER the new sp is built (with sp passed in) so any orphan DOM on
+  // the new sp.root from a previous render is cleared too.
+  disposeVolcanoAttachments();
+
+  const initialMetric: MetricKind = (df.getTag(VOLCANO_METRIC_TAG) as MetricKind | null) ?? 'adj.p-value';
+  df.setTag(VOLCANO_METRIC_TAG, initialMetric);
+
+  const yColName = ensureNegLog10Column(df, initialMetric);
+  const colorColName = ensureDirectionColumn(df, fcThreshold, pThreshold, initialMetric);
+
+  const sp = df.plot.scatter({
+    x: 'log2FC',
+    y: yColName,
+    color: colorColName,
+  });
+
+  applyThresholdLines(df, yColName, fcThreshold, pThreshold);
+  sp.props.showViewerFormulaLines = true;
+
+  // Hide the platform's interactive axis column-selector chips. They render the
+  // raw column name ('log2FC' / 'negLog10P') next to each axis and collided with
+  // our custom rotated axis labels below (the two overlapping Y titles the fix
+  // targets). The `showXSelector`/`showYSelector` props don't suppress them on
+  // the current runtime, so we hide the chips with a scoped stylesheet keyed off
+  // a marker class; the color/size selectors and canvas ticks are untouched.
+  // attachAxisLabels supplies the sole, pretty axis titles.
+  ensureVolcanoStyles();
+  sp.root.classList.add(VOLCANO_ROOT_CLASS);
+
+  // G1 title synthesis — runs AFTER any caller-passed options.title so the
+  // contract is the synthesized string. Callers that need an explicit title
+  // can read the synthesized value back via sp.getOptions().look.title.
+  const title = options?.title ?? synthesizeVolcanoTitle(df);
+  sp.setOptions({title});
+
+  attachAxisLabels(sp, df);
+  attachCounterOverlay(sp, df);
+  applyVolcanoAxisBounds(sp, df);
+
+  // D-03 (decoupled): label the top-N by significance via the sparse label
+  // column — NOT via df.selection. topNLabels=0 opts out (no labels).
+  applyTopNLabels(df, sp, options?.topNLabels ?? 15);
+
+  return sp;
+}
+
+/** Single synchronized recompute: re-runs the metric-parameterized Y and
+ * direction helpers and the threshold lines together, then points the scatter
+ * at the chosen color dimension. After a Q↔P toggle the Y values, up/down/NS
+ * classes and the threshold line all move together — they never disagree.
+ * `colorDim`: 'significance' → direction column, 'location' → the locked
+ * Subcellular-Location palette. `metric` 'p-value' is guarded (falls back to
+ * adj.p-value when the column is absent). */
+export async function recomputeVolcano(
+  df: DG.DataFrame,
+  sp: DG.ScatterPlotViewer,
+  metric: MetricKind,
+  colorDim: ColorDim,
+  fcThreshold = DEFAULT_FC_THRESHOLD,
+  pThreshold = DEFAULT_P_THRESHOLD,
+  progress?: ProgressCb,
+): Promise<void> {
+  // Persist BEFORE the column-recompute path so the axis-label refresh below
+  // sees the new metric. The tag is the single source of truth for G2.
+  df.setTag(VOLCANO_METRIC_TAG, metric);
+
+  const yName = ensureNegLog10Column(df, metric);
+  const dirName = ensureDirectionColumn(df, fcThreshold, pThreshold, metric);
+  applyThresholdLines(df, yName, fcThreshold, pThreshold);
+
+  sp.props.xColumnName = 'log2FC';
+  sp.props.yColumnName = yName;
+  if (colorDim === 'location')
+    sp.props.colorColumnName = await ensureLocationColumn(df, progress);
+  else
+    sp.props.colorColumnName = dirName;
+
+  refreshVolcanoAxisLabel(sp, df);
+  applyVolcanoAxisBounds(sp, df);
+}