figure-ed6-ed7-singlecell-mouse

Metadata

Status	done
Assigned	`agent-705`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-05-05T05:04:28.157530953+00:00
Started	2026-05-05T05:49:03.588559018+00:00
Completed	2026-05-05T05:57:04.472822326+00:00
Tags	`paper-prep,figure`, `eval-scheduled`
Tokens	5379598 in / 31129 out
Eval score	0.27
└ blocking impact	0.20
└ completeness	0.20
└ constraint fidelity	0.85
└ coordination overhead	0.30
└ correctness	0.25
└ downstream usability	0.10
└ efficiency	0.35
└ intent fidelity	0.54
└ style adherence	0.50

Description

Produce ED6 (single-cell 3D + RPE-1, 4 panels) and ED7 (mouse cross-species, 4 panels). Implement directly — do not decompose further.

File scope

paper_prep/figures/ed6/figure_ed6.{pdf,png,R/py}, caption.md, sources.tsv
paper_prep/figures/ed7/figure_ed7.{pdf,png,R/py}, caption.md, sources.tsv

Figure spec (excerpt from MANUSCRIPT_SKELETON.md ED6, ED7)

ED6 — Single-cell 3D + RPE-1

Panel	Content	Status	Source
ED6a	GM12878 Dip-C Mantel scatter + radial-by-community	READY	`gm12878_mantel_scatter.pdf` + `gm12878_radial_community.pdf` — `SURVEY_06 §2`
ED6b	Sperm Mantel scatter + per-cell W/B + radial	READY	`sperm_all20_mantel_scatter.pdf` + `sperm_all20_radial_community.pdf` — `SURVEY_06 §2`
ED6c	Per-arm radial positions (46 arms; S1/S2/S7 peripheral; cis-arm proximity)	GENERATE	§1.4 table in `SURVEY_06`
ED6d	RPE-1 self-discovered cell-cycle modulation (async vs mitotic, 3 datasets, all 5 resolutions)	READY/composite	`RPE1_subtelo/hic_validation/{res}bp/` — `SURVEY_09 §1.4`

ED7 — Mouse cross-species generalisation

Panel	Content	Status	Source
ED7a	Mouse 27-arm Leiden 2-community map vs human 41-arm 15-community	GENERATE	`mouse_T2T/similarity_1Mb/mouse.arm-leiden.communities.tsv` + human equivalent — `SURVEY_08 §6 T-5`
ED7b	Mouse window-size scaling (1/2/4/10/15/33 Mb) — PHR size + saturation fraction	GENERATE	`subtelo_{N}Mb/mouse.all-vs-all.p95.id95.len.tsv` — `SURVEY_08 §6 T-3`
ED7c	Mouse B/W & Mantel ρ across 4 stages × 5 resolutions × 3 windows	READY/composite	`community_analysis_{1,2,4}Mb/{res}bp/zuo2021_*_global_test.tsv`
ED7d	Mouse private-pair → human syntenic-net (mm39→hg38, all in human interiors)	GENERATE	mm39→hg38 syntenic net + `SURVEY_08 §1.6` table

Validation

All 8 panels; sources.tsv per ED
Captions ≤ 200 words each
PDF + PNG per ED

Inputs

paper_prep/synthesis/MANUSCRIPT_SKELETON.md
paper_prep/surveys/SURVEY_06_dipc_validation.md, SURVEY_08_mouse.md, SURVEY_09_rpe1_self.md

## Description
Produce ED6 (single-cell 3D + RPE-1, 4 panels) and ED7 (mouse cross-species, 4 panels). Implement directly — do not decompose further.

## File scope
- `paper_prep/figures/ed6/figure_ed6.{pdf,png,R/py}`, `caption.md`, `sources.tsv`
- `paper_prep/figures/ed7/figure_ed7.{pdf,png,R/py}`, `caption.md`, `sources.tsv`

## Figure spec (excerpt from MANUSCRIPT_SKELETON.md ED6, ED7)

### ED6 — Single-cell 3D + RPE-1
| Panel | Content | Status | Source |
|---|---|---|---|
| ED6a | GM12878 Dip-C Mantel scatter + radial-by-community | READY | `gm12878_mantel_scatter.pdf` + `gm12878_radial_community.pdf` — `SURVEY_06 §2` |
| ED6b | Sperm Mantel scatter + per-cell W/B + radial | READY | `sperm_all20_mantel_scatter.pdf` + `sperm_all20_radial_community.pdf` — `SURVEY_06 §2` |
| ED6c | Per-arm radial positions (46 arms; S1/S2/S7 peripheral; cis-arm proximity) | GENERATE | §1.4 table in `SURVEY_06` |
| ED6d | RPE-1 self-discovered cell-cycle modulation (async vs mitotic, 3 datasets, all 5 resolutions) | READY/composite | `RPE1_subtelo/hic_validation/{res}bp/` — `SURVEY_09 §1.4` |

### ED7 — Mouse cross-species generalisation
| Panel | Content | Status | Source |
|---|---|---|---|
| ED7a | Mouse 27-arm Leiden 2-community map vs human 41-arm 15-community | GENERATE | `mouse_T2T/similarity_1Mb/mouse.arm-leiden.communities.tsv` + human equivalent — `SURVEY_08 §6 T-5` |
| ED7b | Mouse window-size scaling (1/2/4/10/15/33 Mb) — PHR size + saturation fraction | GENERATE | `subtelo_{N}Mb/mouse.all-vs-all.p95.id95.len.tsv` — `SURVEY_08 §6 T-3` |
| ED7c | Mouse B/W & Mantel ρ across 4 stages × 5 resolutions × 3 windows | READY/composite | `community_analysis_{1,2,4}Mb/{res}bp/zuo2021_*_global_test.tsv` |
| ED7d | Mouse private-pair → human syntenic-net (mm39→hg38, all in human interiors) | GENERATE | mm39→hg38 syntenic net + `SURVEY_08 §1.6` table |

## Validation
- [ ] All 8 panels; sources.tsv per ED
- [ ] Captions ≤ 200 words each
- [ ] PDF + PNG per ED

## Inputs
- `paper_prep/synthesis/MANUSCRIPT_SKELETON.md`
- `paper_prep/surveys/SURVEY_06_dipc_validation.md`, `SURVEY_08_mouse.md`, `SURVEY_09_rpe1_self.md`

Depends on

Required by

Log

2026-05-05T05:49:03.588562906+00:00 Spawned by coordinator --executor claude --model opus
2026-05-05T05:49:25.353531949+00:00 Starting work — inspecting inputs and prior figure patterns
2026-05-05T05:52:24.942533775+00:00 Inputs surveyed; data files identified for all 8 panels. Drafting R scripts for ED6 and ED7.
2026-05-05T05:57:04.472827105+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-05T06:04:15.408188985+00:00 PendingEval → Done (evaluator passed; downstream unblocks)