review-zoom-hic-figure-redesign

Metadata

Status	done
Assigned	`agent-970`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-06T20:28:34.598785325+00:00
Started	2026-05-06T20:43:54.715404712+00:00
Completed	2026-05-06T21:05:20.888735694+00:00
Tags	`bog-this-week`, `bog-deck`, `review-zoom`, `revision-fanout`, `git-provenance`, `eval-scheduled`
Eval score	0.93
└ blocking impact	0.97
└ completeness	0.90
└ constraint fidelity	0.85
└ coordination overhead	0.96
└ correctness	0.92
└ downstream usability	0.92
└ efficiency	0.96
└ intent fidelity	0.81
└ style adherence	0.94

Description

User review points 12, 13, 16, 17, and 18.

Goal: propose and generate better visual treatments for the 3D evidence slides: slide 10a matrix should be 1:1, 10b Mantel exclusions needs clear interpretation, slide 11 single-cell 3D needs a readable purpose, slide 12a mouse meiotic Hi-C needs explanation, and slide 12b trajectory inset has oversized typography.

Critical provenance requirement:

First read the upstream review-zoom-git-provenance-audit output and use git history (git log, git show, git blame) to identify when these Hi-C assets/scripts entered the repo and which commits changed them.

Requirements:

Use the methods glossary task as conceptual input if available, but do not block on it; inspect the same source scripts directly.
For slide 10a, produce or specify a square 1:1 contact matrix crop/layout with preserved labels/color scale.
For slide 10b, redesign labeling around full-arm-set vs excluding acrocentric+sex arms and explain what movement above y=x means.
For slide 11, recommend whether to keep current Fig 3c, split into a simpler single-cell Mantel slide, or add a short explanatory title/subtitle.
For slide 12a/b, propose a readable mouse zygotene plus stage trajectory pairing with smaller font and less visual dominance.
Keep outputs isolated; final integration will decide.

Deliverables:

Candidate assets/mockups under slides/v2-review-zoom/_revision_assets/hic_visual_redesign/.
Markdown with exact slide replacements, caption/title text, and git/source provenance.

User review points 12, 13, 16, 17, and 18.

Critical provenance requirement:
- First read the upstream `review-zoom-git-provenance-audit` output and use git history (`git log`, `git show`, `git blame`) to identify when these Hi-C assets/scripts entered the repo and which commits changed them.

Requirements:
- Use the methods glossary task as conceptual input if available, but do not block on it; inspect the same source scripts directly.
- For slide 10a, produce or specify a square 1:1 contact matrix crop/layout with preserved labels/color scale.
- For slide 10b, redesign labeling around full-arm-set vs excluding acrocentric+sex arms and explain what movement above y=x means.
- For slide 11, recommend whether to keep current Fig 3c, split into a simpler single-cell Mantel slide, or add a short explanatory title/subtitle.
- For slide 12a/b, propose a readable mouse zygotene plus stage trajectory pairing with smaller font and less visual dominance.
- Keep outputs isolated; final integration will decide.

Deliverables:
- Candidate assets/mockups under `slides/v2-review-zoom/_revision_assets/hic_visual_redesign/`.
- Markdown with exact slide replacements, caption/title text, and git/source provenance.

Depends on

Required by

Log

2026-05-06T20:28:34.576226610+00:00 Task paused
2026-05-06T20:28:35.239687922+00:00 Task published
2026-05-06T20:43:54.715408459+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-06T20:44:15.988933783+00:00 Starting Hi-C visual redesign documentation and provenance review
2026-05-06T20:46:45.198550653+00:00 Read provenance audit and source scripts; confirmed methods glossary task is unavailable/open, continuing from direct scripts
2026-05-06T20:55:50.947636922+00:00 Generated initial Hi-C redesign candidate PNGs from source data and current figure scripts
2026-05-06T21:03:21.812123884+00:00 Wrote README with exact replacements, caption/title text, and git/source provenance
2026-05-06T21:03:44.414316330+00:00 Validated generated assets: 10a is square 1800x1800; 10b/11/12 are 1800x1200; visual checks completed
2026-05-06T21:04:12.117113252+00:00 Validated: R generator runs, README addresses all requested slide replacements/provenance, and git diff --cached --check passes
2026-05-06T21:04:46.577227258+00:00 Committed: f421645 — pushed to origin/wg/agent-970/review-zoom-hic-figure-redesign
2026-05-06T21:05:03.850074339+00:00 Committed: f421645 - pushed to origin/wg/agent-970/review-zoom-hic-figure-redesign
2026-05-06T21:05:20.888744230+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-06T21:12:20.170900847+00:00 PendingEval → Done (evaluator passed; downstream unblocks)