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figure-4-pedigree-mouse

Figure 4: pedigree-resolved exchanges + cross-species mouse generalisation

Metadata

Statusdone
Assignedagent-693
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-05-05T04:55:48.201296368+00:00
Started2026-05-05T05:28:02.524573352+00:00
Completed2026-05-05T05:49:09.140137363+00:00
Tagspaper-prep,figure, eval-scheduled
Eval score0.88
└ blocking impact0.95
└ completeness0.98
└ constraint fidelity0.85
└ coordination overhead0.80
└ correctness0.95
└ downstream usability0.92
└ efficiency0.65
└ intent fidelity0.92
└ style adherence0.70

Description

Description

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

File scope

  • paper_prep/figures/fig4/figure_fig4.{pdf,png}
  • paper_prep/figures/fig4/figure_fig4.{R,py}
  • paper_prep/figures/fig4/caption.md
  • paper_prep/figures/fig4/sources.tsv

Figure spec (excerpt from MANUSCRIPT_SKELETON.md §Figure 4)

Figure 4 — Pedigree-resolved exchanges and cross-species generalisation

Caption. Direct observation of the events that build the communities, in human pedigrees and across mammals. (a) WashU 3-generation untangle ribbons (PAN027 maternal hap1 from PAN010, PAN028 maternal hap1 from PAN027) with off-diagonal inter-chr patches highlighted; 92 % of 538 HQ patches sit in a Leiden community. (b) Cross-assembler-validated CEPH1463 4-gen parent-feature matrix (11 robust events; hifiasm + verkko intersection); chr10/chr18 (C2/Linardopoulou) detected in NA12877 paternal and NA12878 maternal independently. (c) RPE-1 t(X;10) rediscovery — pipeline run on a single diploid individual partitions chr10_q with chrX_q (community C2), confirming the known translocation from sequence alone. (d) Mouse cross-species generalisation — zygotene per-PHR-pair similarity vs Hi-C contact, ρ = 0.715, p = 4.4e-55; same correlation across all 4 meiotic stages, B6 + CAST T2T.

PanelContentStatusSource
4aWashU PAN027 + PAN028 untangle ribbonsREADYend-to-end-report/pedigree-plots/washu/*.untangle.pdf (3 PDFs) — SURVEY_14 §2, SURVEY_FIG_inv §4
4bCEPH1463 cross-assembler 11-feature matrixGENERATE§1.6 table in SURVEY_14; all_pedigrees_patches.tsv filtered
4cRPE-1 t(X;10) positive-control panelGENERATErpe1.dist_matrix.tsv + rpe1_self_async_cifi_contact_matrix.tsv — SURVEY_09 §6 T-1
4dMouse zygotene PHR-pair scatter (1 Mb, 50 kb)READYmouse_T2T/community_analysis_1Mb/50000bp/zuo2021_zygotene_phr_pair_scatter.pdf — SURVEY_08 §2

Validation

  • All 4 panels; sources.tsv complete
  • Caption ≤ 200 words; ≥ 2 metrics with TSV paths
  • PDF + PNG

Inputs

  • paper_prep/synthesis/MANUSCRIPT_SKELETON.md
  • paper_prep/surveys/SURVEY_14_pedigree_recombination.md, SURVEY_08_mouse.md, SURVEY_09_rpe1_self.md

Depends on

Required by

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