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fig5-par1-phr-candidate-panels

Fig5 PAR1 and PHR candidate recombination panels

Metadata

Statusdone
Assignedagent-2572
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-19T20:43:44.265713936+00:00
Started2026-06-19T20:45:09.260836737+00:00
Completed2026-06-19T20:55:03.140782829+00:00
Tagspedigree, figure, sweepga, manuscript-candidate, eval-scheduled
Eval score0.90
└ blocking impact0.95
└ completeness0.93
└ constraint fidelity0.10
└ coordination overhead0.92
└ correctness0.86
└ downstream usability0.86
└ efficiency0.95
└ intent fidelity0.92
└ style adherence0.90

Description

Build a compact candidate Figure 5 asset pack that combines the best pedigree recombination examples now visible in the sweepGA/untangle outputs. This is a presentation/figure task, not a new biological-discovery pipeline and not a manuscript rewrite.

Objective: Create a reproducible 4-5 panel candidate figure under paper_prep/_brainstorming/fig5_par1_phr_candidate_panels/ showing: (1) the paternal PAR1 positive-control recombination; (2) the strongest PAN027 autosomal PHR candidate; (3) an independent PAN028 autosomal PHR candidate; optionally (4) one known-system/acrosome-like PHR panel only if it is legible and does not turn into an acrocentric p-arm hairball; and (5) a small overview strip/table of the finite selected candidate set. Use the same restrained visual language as the submitted/native untangle-style redraws where possible. Avoid 23 indistinguishable chromosome colors; highlight the non-homologous donor arms clearly and subdue uninformative same-chromosome background.

Key event candidates to evaluate and show:

  • Positive control: PAN027 paternal (hap2) vs PAN011 (father), query PAN027#2#chrX.paternal:12265-512264_chrX_parm. The main PAR1 signal is chrX p -> chrYp, 0-143431, mean score 0.9998, min score 0.9933, community C15/C15, within-community. Treat this as a known male PAR1 X/Y recombination sanity check, not evidence for novel autosomal PHR exchange. The smaller chrYp intervals at 189599-194850 and 329647-331663 can be shown or annotated if they help explain the path, but do not overemphasize them.
  • PAN027 autosomal PHR candidate: PAN027 paternal (hap2) vs PAN011 (father), query PAN027#2#chr9.paternal:135704825-136204824_chr9_qarm. Terminal block switches from chr9q into mostly chr3q: 446944-472441 chr3q h2 mean/min 0.9975/0.9963; 476266-491186 chr3q h2 0.9768/0.9768; 498459-499507 chr3q h2 0.9801/0.9801. The 491186-498459 chr15q h1 piece is real but cross-community C3/C8 and should be visually marked as secondary. The tiny 499507-500000 chr20q tail is low score/small and should be subdued, filtered, or explicitly labeled low-confidence if included. Describe this as a candidate terminal PHR exchange patch, not a clean full crossover.
  • Independent autosomal support: PAN028 maternal (hap1) vs PAN027 (mother), query PAN028#1#chr3.haplotype1:199233840-199733839_chr3_qarm, with the strongest chr9q h2 intervals: 390073-407837 mean/min 0.9991/0.9991 and 409115-470323 mean/min 0.9978/0.9909, plus smaller same-community intervals if needed. This should show that the chr3/chr9 C3 signal is not just one odd PAN027 panel.
  • Optional known-system panel: choose only if legible. Candidate examples include acrocentric p-arm C7 within-community blocks or another clean high-confidence PHR example. Do not let this panel dominate or obscure the PAR1 + autosomal PHR story.

Required outputs:

  • A reproducible plotting script, preferably in scripts/pedigree/ if it is generally reusable, or inside the brainstorming directory if it is explicitly experimental. Document command-line usage.
  • paper_prep/_brainstorming/fig5_par1_phr_candidate_panels/fig5_par1_phr_candidate_panels.pdf and .svg; PNG optional if useful.
  • panel_event_summary.tsv listing each panel, transmission, query, donor arm(s), interval(s), score(s), community status, PHR/PAR status, and whether the event is positive-control / autosomal-candidate / secondary fragment / low-confidence.
  • README.md explaining provenance, exact input files, regeneration command, and interpretation boundaries.

Constraints:

  • Do not edit submission/paper.tex, submission/fig/MainFigures/Fig5_pedigree_untangle.pdf, or bibliography files in this task. This is a candidate asset pack for review before manuscript integration.
  • Do not invent new analyses or rerun heavy untangle/sweepGA jobs on the head node. Use existing outputs. If a missing input requires heavy computation, write an sbatch script and stop with clear instructions rather than running it interactively.
  • Preserve cautious language for pedigree event-level claims: use candidate / compatible with / positive control. The PAR1 panel can be assertive as a known positive control, but keep it separate from the novel autosomal PHR interpretation.
  • Avoid saturated many-color palettes. Use a small semantic palette: same-chromosome background neutral; PAR1 chrY donor highlighted; chr3/chr9 PHR candidate donors highlighted; secondary/cross-community fragments subdued.
  • Before completing, inspect generated PDFs/SVGs enough to ensure labels are legible and no off-panel fragments or coordinate bugs remain.

Validation:

  • Figure PDF and SVG exist in the requested brainstorming directory.
  • panel_event_summary.tsv and README.md exist and match the plotted panels.
  • The PAR1 positive control and both autosomal chr9q/chr3q or chr3q/chr9q candidate panels are included.
  • Same-chromosome background is visually subdued; non-homologous donor arms are visually clear; no 23-color chromosome legend is required to read the figure.
  • The task does not modify the submitted manuscript or replace the submitted Fig5 asset.
  • Any code/data changes are committed using the project convention feat: fig5-par1-phr-candidate-panels (agent-NNN).

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