figure-ed3-ed4-annotation-genes

Metadata

Status	done
Assigned	`agent-697`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-05-05T05:00:06.303863688+00:00
Started	2026-05-05T05:28:15.929325549+00:00
Completed	2026-05-05T05:42:15.183716253+00:00
Tags	`paper-prep,figure`, `eval-scheduled`
Eval score	0.88
└ blocking impact	0.90
└ completeness	0.90
└ constraint fidelity	0.85
└ coordination overhead	0.85
└ correctness	0.85
└ downstream usability	0.90
└ efficiency	0.85
└ intent fidelity	0.94
└ style adherence	0.90

Description

Produce ED3 (4 panels) annotation and ED4 (4 panels) gene enrichment. Implement directly — do not decompose further.

File scope

paper_prep/figures/ed3/figure_ed3.{pdf,png,R/py}, caption.md, sources.tsv
paper_prep/figures/ed4/figure_ed4.{pdf,png,R/py}, caption.md, sources.tsv

Figure spec (excerpt from MANUSCRIPT_SKELETON.md ED3, ED4)

ED3 — Annotation: TAR1 + internal (TTAGGG)n + telomere length

Panel	Content	Status	Source
ED3a	TAR1 prevalence per arm (PAR1 absence; acrocentric intermediate; autosomal saturation)	GENERATE	`community_tar1_by_arm.tsv` — `SURVEY_02 §6 Fig M1a`
ED3b	Internal (TTAGGG)n island length distribution + canonical-fraction histogram	GENERATE	`length_distribution.tsv` + `motif_composition.tsv` — `SURVEY_02 §6 Fig M2`
ED3c	Terminal telomere length by community (Kruskal-Wallis H = 100.89, p = 3.2e-15)	GENERATE	`.telo.tsv` joined to community assignments — `SURVEY_02 §6 ED3`
ED3d	Per-arm TAR1 positional distance-from-telomere	GENERATE	`tar1_positional_per_arm.tsv` — `SURVEY_02 §6 Fig M1b`

ED4 — Gene enrichment, pseudogene gradient, copy-weighted GO

Panel	Content	Status	Source
ED4a	GSEA / GO:BP top terms (snRNP, olfactory, sensory) — vertical bar	READY	`Figure1_GSEA_BP_vertical.pdf` (1 Mb caveat — flag PHR-only re-run) — `SURVEY_FIG_inv §3`
ED4b	Copy-weighted vs deduplicated comparison (olfactory fold = 598)	GENERATE	`improved_copy_weighted_vs_deduplicated_comparison.csv` — `SURVEY_DATA §4`
ED4c	High-copy gene families (DUX4 ×18, BAGE2, MTCO, RPL23A, SEPTIN14P22, OR4F)	GENERATE	`gene_copy_summary.csv` — `SURVEY_DATA §2`
ED4d	OR4F pseudogenisation gradient (62.1 % pseudogene; 11.1 % chr7_p → 99.8 % chr15_q)	GENERATE	per-arm pseudogene fraction — `SURVEY_10/11/12 C12`

Validation

All 8 panels; sources.tsv per ED
Captions ≤ 200 words; ≥ 2 metrics with TSV paths
PDF + PNG per ED
ED4a caption notes 1 Mb window caveat (PHR-only re-run flagged in WORK_DECOMPOSITION.md ## Gaps)

Inputs

paper_prep/synthesis/MANUSCRIPT_SKELETON.md
paper_prep/surveys/SURVEY_02_annotation.md, SURVEY_DATA_inventory.md, SURVEY_10_11_12_limits_summary_lit.md

## Description
Produce ED3 (4 panels) annotation and ED4 (4 panels) gene enrichment. Implement directly — do not decompose further.

## File scope
- `paper_prep/figures/ed3/figure_ed3.{pdf,png,R/py}`, `caption.md`, `sources.tsv`
- `paper_prep/figures/ed4/figure_ed4.{pdf,png,R/py}`, `caption.md`, `sources.tsv`

## Figure spec (excerpt from MANUSCRIPT_SKELETON.md ED3, ED4)

### ED3 — Annotation: TAR1 + internal (TTAGGG)n + telomere length
| Panel | Content | Status | Source |
|---|---|---|---|
| ED3a | TAR1 prevalence per arm (PAR1 absence; acrocentric intermediate; autosomal saturation) | GENERATE | `community_tar1_by_arm.tsv` — `SURVEY_02 §6 Fig M1a` |
| ED3b | Internal (TTAGGG)n island length distribution + canonical-fraction histogram | GENERATE | `length_distribution.tsv` + `motif_composition.tsv` — `SURVEY_02 §6 Fig M2` |
| ED3c | Terminal telomere length by community (Kruskal-Wallis H = 100.89, p = 3.2e-15) | GENERATE | `.telo.tsv` joined to community assignments — `SURVEY_02 §6 ED3` |
| ED3d | Per-arm TAR1 positional distance-from-telomere | GENERATE | `tar1_positional_per_arm.tsv` — `SURVEY_02 §6 Fig M1b` |

### ED4 — Gene enrichment, pseudogene gradient, copy-weighted GO
| Panel | Content | Status | Source |
|---|---|---|---|
| ED4a | GSEA / GO:BP top terms (snRNP, olfactory, sensory) — vertical bar | READY | `Figure1_GSEA_BP_vertical.pdf` (1 Mb caveat — flag PHR-only re-run) — `SURVEY_FIG_inv §3` |
| ED4b | Copy-weighted vs deduplicated comparison (olfactory fold = 598) | GENERATE | `improved_copy_weighted_vs_deduplicated_comparison.csv` — `SURVEY_DATA §4` |
| ED4c | High-copy gene families (DUX4 ×18, BAGE2, MTCO, RPL23A, SEPTIN14P22, OR4F) | GENERATE | `gene_copy_summary.csv` — `SURVEY_DATA §2` |
| ED4d | OR4F pseudogenisation gradient (62.1 % pseudogene; 11.1 % chr7_p → 99.8 % chr15_q) | GENERATE | per-arm pseudogene fraction — `SURVEY_10/11/12 C12` |

## Validation
- [ ] All 8 panels; sources.tsv per ED
- [ ] Captions ≤ 200 words; ≥ 2 metrics with TSV paths
- [ ] PDF + PNG per ED
- [ ] ED4a caption notes 1 Mb window caveat (PHR-only re-run flagged in WORK_DECOMPOSITION.md ## Gaps)

## Inputs
- `paper_prep/synthesis/MANUSCRIPT_SKELETON.md`
- `paper_prep/surveys/SURVEY_02_annotation.md`, `SURVEY_DATA_inventory.md`, `SURVEY_10_11_12_limits_summary_lit.md`

Depends on

Required by

Log

2026-05-05T05:28:15.929329366+00:00 Spawned by coordinator --executor claude --model opus
2026-05-05T05:29:03.805680573+00:00 Starting: figures dir does not exist; surveys + synthesis present. Will create paper_prep/figures/ed3 and ed4 with 4 panels each.
2026-05-05T05:39:12.276124569+00:00 Built ED3 (4 panels: TAR1 prevalence, TTAGGG length+motif, telomere length by community, TAR1 distance) and ED4 (4 panels: GO:BP, copy-weighted vs dedup, high-copy families, OR4F gradient). PDF + PNG rendered. caption.md + sources.tsv present.
2026-05-05T05:42:09.353806766+00:00 Validated: 8 panels rendered (4 ED3 + 4 ED4), PDF+PNG per ED, captions <=200 words with source TSV paths cited inline, sources.tsv per ED, ED4a notes 1 Mb caveat. Committed: 438fb02 -- pushed to origin/wg/agent-697/figure-ed3-ed4-annotation-genes.
2026-05-05T05:42:15.183720471+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-05T05:56:25.317025367+00:00 PendingEval → Done (evaluator passed; downstream unblocks)