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figure-3-3d-convergence

Figure 3: 3D nuclear organisation mirrors sequence communities

Metadata

Statusdone
Assignedagent-700
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-05-05T04:53:45.495337936+00:00
Started2026-05-05T05:31:18.399138682+00:00
Completed2026-05-05T05:52:07.448355434+00:00
Tagspaper-prep,figure, eval-scheduled
Eval score0.84
└ blocking impact0.85
└ completeness0.80
└ constraint fidelity0.85
└ coordination overhead0.90
└ correctness0.80
└ downstream usability0.85
└ efficiency0.85
└ intent fidelity0.92
└ style adherence0.90

Description

Description

Produce Main Fig 3 (4 panels). Implement directly — do not decompose further.

File scope

  • paper_prep/figures/fig3/figure_fig3.{pdf,png}
  • paper_prep/figures/fig3/figure_fig3.{R,py}
  • paper_prep/figures/fig3/caption.md
  • paper_prep/figures/fig3/sources.tsv

Figure spec (excerpt from MANUSCRIPT_SKELETON.md §Figure 3)

Figure 3 — Three-dimensional nuclear organisation mirrors sequence communities

Caption. Sequence-defined communities are physical. (a) HG002 Pore-C inter-chromosomal contact matrix at 50 kb, arms ordered by sequence community; diagonal blocks visibly enriched (B/W = 0.056, p = 3.9e-85). (b) Convergent-evidence forest plot — 14 independent tests across Hi-C, Pore-C, CiFi, Dip-C, sperm scHi-C, mouse meiotic Hi-C; all on the within-community-stronger side of unity. (c) Negative-control panel — S_all (7 non-sharing arms): 0/16 GM12878 + 1/20 sperm cells fall below W/B = 1, vs 16/16 + 19/20 for C-communities; 11 % / 40 % farther in 3D. (d) Flanking paradox — 100 kb centromere-ward of PHR is unique sequence yet gives stronger signal (HG002 flanking B/W 0.002 vs PHR 0.027; 13×).

PanelContentStatusSource
3aHG002 Pore-C / Hi-C contact matrix grouped by communityREADYhg002_porec_hic_community_heatmap.pdf — SURVEY_05 §2.1
3bConvergent-evidence forest plot (14 tests × 6 technologies)GENERATE<sample>_global_test.tsv × 8 + Dip-C/sperm/RPE-1/mouse summaries — SURVEY_07 §6 T-1
3cS_all negative-control + per-cell W/B distributionsGENERATEgm12878_per_community_per_cell.tsv + community_enrichment_16cells_500kb_per_community_per_cell.tsv + sperm equivalent — SURVEY_06 §1.3, §6 T-1, T-4
3dFlanking-vs-PHR B/W panel (8 samples) + Dip-C flanking radial insetGENERATEflanking/{res}bp/<sample>_global_test.tsv + Dip-C flanking radial 0.503 vs 0.551 — SURVEY_07 §6 T-5

Validation

  • All 4 panels; sources.tsv complete
  • Caption ≤ 200 words; ≥ 2 metrics with TSV paths
  • PDF + PNG
  • B/W convention vs W/B convention disambiguated in caption (SURVEY_07 §5 #11)

Inputs

  • paper_prep/synthesis/MANUSCRIPT_SKELETON.md
  • paper_prep/surveys/SURVEY_05_hic_validation.md, SURVEY_06_dipc_validation.md, SURVEY_07_integrated.md

Depends on

Required by

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