Commit 6ed117f
IGV normalization explanation: causal report + LegNet stub parity
Final pre-ship verification: 17 shipped HTML reports audited for
(a) IGV embedded, (b) signal tracks floor-rescaled to [0, 3.0],
(c) user-facing "noise floor (p95) / peak threshold (p99)"
explanation next to the IGV block, (d) track labels carry
assay:cell_type provenance (oracle · assay:cell_type for multi-oracle).
Two reports failed before this fix:
1. causal_prioritization/SORT1_locus causal report — 65/67 tracks
were already floor-rescaled to ymax=3.0 (the 2 outliers are
"Sentinel" + "Composite Score" summary tracks, correctly [0,1]),
but the scale explanation block from variant_report.py wasn't
replicated in causal.py. Added the same <p> note directly after
the existing IGV intro paragraph (chorus/analysis/causal.py:1190).
2. validation/SORT1_rs12740374_multioracle/rs12740374_SORT1_legnet_report.html
— stale from before the multi-oracle regen flow started
persisting _normalizer through to_dict/from_dict.
Re-ran scripts/regenerate_multioracle.py --oracle legnet (and
--consolidate to keep the unified report in sync). LegNet stub
now shows the floor/p99 block and uses the rescaled axis.
Result: 17/17 HTMLs pass the 4-part audit. Track provenance verified:
every single-oracle track label is {assay}:{cell_type}; every
multi-oracle track label is {oracle} · {assay}:{cell_type}. Every
IGV y-axis is either 3.0 (signal tracks, floor-rescaled) or 1.0
(summary/composite tracks, [0,1] by construction). No raw-autoscale
leaks.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>1 parent 5300daa commit 6ed117f
10 files changed
Lines changed: 339 additions & 329 deletions
File tree
- chorus/analysis
- examples/walkthroughs
- causal_prioritization/SORT1_locus
- validation/SORT1_rs12740374_multioracle
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