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review-zoom-v5-enrichment-fanin-render

Render review zoom v5 with copy-number-aware gene enrichment slides

Metadata

Statusdone
Assignedagent-1073
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-05-07T15:04:04.157894928+00:00
Started2026-05-07T15:46:44.026820172+00:00
Completed2026-05-07T16:10:12.179828575+00:00
Tagsreview-zoom, review-zoom-v5, gene-enrichment, copy-number, fanin, render, eval-scheduled
Eval score0.94
└ blocking impact0.93
└ completeness0.94
└ constraint fidelity0.25
└ coordination overhead0.92
└ correctness0.95
└ downstream usability0.96
└ efficiency0.88
└ intent fidelity0.74
└ style adherence0.94

Description

Synthesize review-zoom v5 by adding a concise copy-number-aware gene enrichment section to the v4 deck and incorporating the v5 slide 07a tree-then-community heatmap pair.

Depends on:

  • review-zoom-v5-copy-number-enrichment-figures
  • review-zoom-v5-copy-number-enrichment-narrative
  • review-zoom-v5-07a-tree-community-heatmaps

Goal:

  • Start from the current v4 review-zoom deck and render a v5 deck with a small gene enrichment section.
  • Preserve the v4 slide 10a X-axis orientation fix and all other v4 changes.
  • Add the slide 07a story as two sequential slides: first the tree/UPGMA-ordered heatmap with side tree, then the same matrix sorted/grouped by community with no tree and clear community boxes/bands.
  • Do not make a broad redesign. Add/replace only what is needed to make the copy-number-aware enrichment and tree-to-community story visible and understandable.

Implementation guidance:

  • Use slides/v2-review-zoom/BoG_2026_review_zoom_v4.pdf and slides/v2-review-zoom/_typst/zoom_review_deck.typ as the base.
  • Use assets from _revision_assets/v5/gene_enrichment_figures/, text from _revision_assets/v5/gene_enrichment_narrative/, and heatmaps from _revision_assets/v5/07a_tree_then_community_heatmap/.
  • For the two heatmap slides, keep the same heatmap color scale/palette across tree and community views. Use the v5 assets with larger arm labels (~1.5x vs the fuzzy earlier version) so chromosome labels are readable.
  • Add 2-4 enrichment slides or replace weak gene-biology slides if that is cleaner. Favor talk clarity over completeness.
  • Keep explicit caveat language: some community-assigned arms do not have called CHM13 PHR intervals in chm13.phrs.bed; do not imply all community arms have rendered/called PHRs.
  • If slide numbering changes, update revision notes and page PNG exports.

Deliverables:

  • slides/v2-review-zoom/BoG_2026_review_zoom_v5.pdf
  • slides/v2-review-zoom/REVISION_NOTES_V5.md
  • Updated Typst/source assets under slides/v2-review-zoom/_typst/ and/or _revision_assets/v5/
  • Page PNG exports sufficient to inspect new slides, both new 07a heatmap slides, enrichment slides, and any changed surrounding slides

Validation

  • v5 PDF renders successfully.
  • v5 contains the two-step slide 07a heatmap sequence: tree/UPGMA ordered with side tree, then community sorted without tree and with community boxes/bands.
  • Heatmap labels are visibly larger/readable and both heatmap slides use the same color scale/palette.
  • v5 contains a visible copy-number-aware gene enrichment section with 2-4 talk-usable slides.
  • v4 slide 10a X-axis orientation fix remains in place; do not regress to the mirrored v3 asset.
  • New enrichment slides include method/caveat language and do not overclaim exploratory/stale outputs.
  • At least the new slides and slide 10a page PNGs render nonblank.
  • REVISION_NOTES_V5.md explains what changed from v4 and lists source assets.
  • git diff --check passes.
  • No stale .wg-worktrees absolute paths are embedded under slides/v2-review-zoom.

Depends on

Required by

✉ Messages 2 messages (2 unread)

  1. #1user2026-05-07T15:13:30.991421271+00:00delivered
    Additional v5 requirement from Erik: include the 07a heatmap story as two sequential slides/assets from task review-zoom-v5-07a-tree-community-heatmaps. First show the tree-ordered heatmap with side tree; then show the same matrix sorted/grouped by community with no tree and community boxes/bands. Preserve the v4 slide 10a fix and the copy-number-aware enrichment section.
  2. #2review-zoom-v5-enrichment-fanin-render2026-05-07T15:47:08.601002475+00:00read
    Acknowledged the queued v5 requirement: I will include the 07a tree-ordered and community-ordered heatmap slides sequentially, preserve the v4 slide 10a fix, and add the copy-number-aware enrichment section.

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