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fig5-synteny-schematic-review-pack

Fig5 synteny schematic visual review pack

Metadata

Statusdone
Assignedagent-2586
Agent identity289ccc9f03fc7c121a5ab8d685ffd018371bcdac67ceab1d50b03e7347d29155
Created2026-06-20T08:26:44.173409584+00:00
Started2026-06-20T08:55:40.815812673+00:00
Completed2026-06-20T08:59:55.943457999+00:00
Tagspedigree, figure, review, synteny, eval-scheduled
Eval score0.94
└ blocking impact0.97
└ completeness0.93
└ constraint fidelity0.55
└ coordination overhead0.95
└ correctness0.94
└ downstream usability0.92
└ efficiency0.96
└ intent fidelity0.87
└ style adherence0.94

Description

Create a visual-inspection/review pack for the Fig5 synteny recombination schematic prototype. This task should not redesign the figure from scratch; it should make the outputs easy for Erik to inspect and identify any conceptual or visual problems.

Inputs:

  • Schematic full/focus outputs from fig5-synteny-schematic-prototype.
  • Event manifest and selected segments from fig5-synteny-event-manifest.
  • Existing colored/debug views for comparison: paper_prep/_brainstorming/fig5_par1_phr_candidate_panels/fig5_par1_phr_candidate_panels.pdf and paper_prep/_brainstorming/fig5_sweepga_1to1_redraw/fig5_sweepga_1to1_redraw.pdf.

Required outputs under paper_prep/_brainstorming/fig5_synteny_recombination_schematic/:

  • asset_index.md: concise list of every inspectable PDF/SVG/table in this schematic pack, with one-sentence purpose for each.
  • VISUAL_REVIEW.md: short review answering:
    1. Does the schematic show both full chromosome context and focused recombination windows?
    2. Are the three events correct under strict primary-path data: PAR1 positive control plus two PHR candidates?
    3. Are coordinates clearly native assembly coordinates or documented otherwise?
    4. Are flow/ribbon labels clear enough to replace vague color-track interpretation?
    5. Any misleading title/label/scale issue that must be fixed before manuscript integration?
    6. Recommendation: use full view, focus view, combined view, or keep as brainstorming only.

Constraints:

  • Do not edit submission/ or replace Fig5.
  • Do not add new analyses or rerun alignments.
  • Keep review concise and concrete; this is for human inspection, not a long defense.
  • Commit with project convention: feat: fig5-synteny-schematic-review-pack (agent-NNN).

Validation:

  • asset_index.md and VISUAL_REVIEW.md exist.
  • Review explicitly checks the second PHR event against the strict manifest.
  • Review flags any coordinate/scale/title problem rather than papering it over.
  • Manuscript files are untouched.

Depends on

Required by

✉ Messages 2 messages (2 unread)

  1. #1user2026-06-20T08:52:05.673311729+00:00delivered
    Author clarification: explicitly flag the older compact asset paper_prep/_brainstorming/fig5_par1_phr_candidate_panels/fig5_par1_phr_candidate_panels.{pdf,svg} as superseded/misleading for panel C. Under strict nb=1 sweepGA 1:1, the old PAN028 chr3q panel does NOT map chr3q to chr9q; it shows side fragments from chr7p, chr16q h1, and chr20q h2. The corrected schematic event is PAN028 chr9q with chr3q primary donor and chr15q side fragment, as in event_manifest.tsv. Make sure VISUAL_REVIEW.md and asset_index.md state this clearly.
  2. #2fig5-synteny-schematic-review-pack2026-06-20T08:55:50.078601286+00:00read
    Acknowledged — I will explicitly flag the older compact PAR1/PHR candidate panels as superseded/misleading for panel C, and verify the corrected PAN028 chr9q event against event_manifest.tsv.

Log