Multi-oracle report: add missing noise-floor/p99 scale block (6ed117f gap)

lp698 · claude · lp698 · commit 5cd7dae48eab · 2026-04-22T16:14:44.000-04:00
Commit 6ed117f ("IGV normalization explanation: causal report + LegNet stub parity") fixed the causal report and LegNet stub but missed the multi-oracle report, which had its own terser IGV intro. Re-audit of the 4-part IGV contract across all 17 shipped HTMLs found rs12740374_SORT1_multioracle_report.html was missing 4/5 of the scale- explanation markers the other reports ship ("noise floor", "p95", "peak threshold", "rescaled using") — only "p99" appeared, in a different phrasing. ## What users saw Before: the multi-oracle IGV block said only "Signals are floor-rescaled to [0, 3.0] where 1.0 is the genome-wide p99 peak for that assay." No mention of the p95 noise floor or "top 1% of bins" framing that every single-oracle + causal report uses, so users opening the multi-oracle view in isolation got a less-explicit explanation than in the per-oracle reports. ## Fix chorus/analysis/multi_oracle_report.py:712-724 — split the existing single-paragraph intro into two paragraphs: the window/coverage caveat stays, plus the same "noise floor (p95) and peak threshold (p99)" block the single-oracle and causal reports emit. Future regenerations of the multi-oracle HTML will ship the new block automatically. Also hand-patched the shipped examples/walkthroughs/validation/SORT1_rs12740374_multioracle/rs12740374_SORT1_multioracle_report.html to insert the same paragraph at the matching location, since regenerating via scripts/regenerate_multioracle.py --consolidate would also rebuild the IGV section from scratch — but without the prediction pickles (not committed), that rebuild drops the IGV entirely. The hand-patch preserves the existing IGV tracks while adding the new explanation. ## 4-part audit result All 17 IGV-containing HTMLs now pass: - (a) IGV embedded — 17/17 - (b) ymax=3.0 signal tracks / 1.0 summary tracks — 17/17 consistent - (c) scale explanation (5/5 markers) — 17/17 (was 16/17) - (d) assay:cell_type track provenance — 17/17 (bare "SPLICE_SITES" labels on AlphaGenome donor/acceptor/padding tracks are correctly cell-type-agnostic per AG metadata) ## Known follow-up scripts/regenerate_multioracle.py --consolidate from committed JSONs silently drops the IGV section because the per-oracle prediction pickles aren't persisted. Either persist them or mark IGV-rebuild as requiring --oracle runs. Filed as a note; not blocking this fix. Tests: 339 passed / 1 skipped. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
diff --git a/chorus/analysis/multi_oracle_report.py b/chorus/analysis/multi_oracle_report.py
@@ -715,9 +715,17 @@ def _build_multioracle_html(report: "MultiOracleReport") -> str:
             "signal tracks on a single IGV. Default locus is the widest "
             "oracle's prediction window — narrower-window oracles show "
             "blank outside their coverage (expected: LegNet is ~200 bp "
-            "and ChromBPNet ~1 kb while AlphaGenome reaches ±500 kb). "
-            "Signals are floor-rescaled to [0, 3.0] where 1.0 is the "
-            "genome-wide p99 peak for that assay.</p>"
+            "and ChromBPNet ~1 kb while AlphaGenome reaches ±500 kb).</p>"
+        )
+        # Same scale-explanation block the single-oracle + causal reports
+        # ship, so the meaning of the [0, 3.0] y-axis is spelled out
+        # consistently across every IGV view chorus emits.
+        p.append(
+            "<p class='meta' style='margin-top:-.5rem'>Signal rescaled "
+            "using each track's genome-wide noise floor (p95) and peak "
+            "threshold (p99): <b>0</b> = noise floor, <b>1.0</b> = top "
+            "1% of bins genome-wide. Peak shape preserved; tracks "
+            "comparable across cell types.</p>"
         )
         p.append(igv_html)
 
diff --git a/examples/walkthroughs/validation/SORT1_rs12740374_multioracle/rs12740374_SORT1_multioracle_report.html b/examples/walkthroughs/validation/SORT1_rs12740374_multioracle/rs12740374_SORT1_multioracle_report.html
@@ -134,6 +134,7 @@ <h2>Cross-oracle consensus</h2>
 </tbody></table>
 <h2>Cross-oracle genome browser</h2>
 <p class='meta'>All oracles' ref (grey) / alt (coloured) signal tracks on a single IGV. Default locus is the widest oracle's prediction window — narrower-window oracles show blank outside their coverage (expected: LegNet is ~200 bp and ChromBPNet ~1 kb while AlphaGenome reaches ±500 kb). Signals are floor-rescaled to [0, 3.0] where 1.0 is the genome-wide p99 peak for that assay.</p>
+<p class='meta' style='margin-top:-.5rem'>Signal rescaled using each track's genome-wide noise floor (p95) and peak threshold (p99): <b>0</b> = noise floor, <b>1.0</b> = top 1% of bins genome-wide. Peak shape preserved; tracks comparable across cell types.</p>
 
 <div id="igv-multioracle" style="margin: 1rem 0; min-height: 400px;"></div>
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