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review-zoom-v5-copy-number-enrichment-figures

Render copy-number-aware gene enrichment figures for review zoom v5

Metadata

Statusdone
Assignedagent-1065
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Created2026-05-07T15:05:39.303914359+00:00
Started2026-05-07T15:24:27.546228860+00:00
Completed2026-05-07T15:42:09.153808100+00:00
Tagsreview-zoom, review-zoom-v5, gene-enrichment, copy-number, figures, eval-scheduled
Eval score0.90
└ blocking impact0.92
└ completeness0.91
└ constraint fidelity0.85
└ coordination overhead0.90
└ correctness0.88
└ downstream usability0.94
└ efficiency0.87
└ intent fidelity0.83
└ style adherence0.88

Description

Create slide-ready figures/tables for the copy-number-aware gene enrichment section of review-zoom v5.

Depends on:

  • review-zoom-v5-copy-number-enrichment-inventory

Goal:

  • Turn the canonical enrichment signals identified by the inventory into 2-3 clean visual assets for a talk slide section.
  • Keep the assets compact, readable, and honest about what is interval-specific versus arm/community/subtelomere-level.

Implementation guidance:

  • Prefer using canonical TSV/CSV/RDS sources identified by the inventory task.
  • Reuse existing local visual style from slides/v2-review-zoom/_revision_assets/14_gene_enrichment_or4f/ and v4 review-zoom assets where appropriate.
  • Recommended figure directions, subject to inventory findings:
    1. A small method/comparison visual: standard/deduplicated ORA versus copy-number-aware enrichment, focused on why PHR/subtelomeric duplicon biology needs copy accounting.
    2. A ranked signal plot/table for top copy-aware biological terms or families, e.g. OR/OR4F, GTP binding/GTPase/IQSEC3/GTPBP6, DDX11L/WASH/FAM138/RPL23A blocks.
    3. A community/family view linking signals to communities/arms, with explicit notation for arms lacking called CHM13 PHR intervals.
  • Do not overclaim statistical finality if the source is exploratory. Use labels like "copy-aware support" or "copy-number-aware candidate signal" when appropriate.

Deliverables:

  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_figures/README.md
  • slides/v2-review-zoom/_revision_assets/v5/gene_enrichment_figures/make_gene_enrichment_figures.R or equivalent reproducible script
  • 2-3 slide-ready .png and .pdf assets under that directory
  • Supporting TSVs used directly by the figure generator

Validation

  • At least two slide-ready PNG assets and matching PDF assets exist.
  • Figures are readable at slide scale and are not dense manuscript tables pasted into slides.
  • Figure labels distinguish called PHR intervals from broader arm/community/subtelomere signals where relevant.
  • README records exact source tables used and any rejected/stale sources.
  • Re-running the figure script regenerates the assets without manual steps.
  • git diff --check passes.

Depends on

Required by

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