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fig5-synteny-schematic-prototype

Fig5 synteny recombination schematic prototype

Metadata

Statusdone
Assignedagent-2582
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-06-20T08:25:53.545559956+00:00
Started2026-06-20T08:40:16.306722501+00:00
Completed2026-06-20T08:48:55.999306475+00:00
Tagspedigree, figure, synteny, schematic, eval-scheduled
Eval score0.90
└ blocking impact0.94
└ completeness0.87
└ constraint fidelity0.10
└ coordination overhead0.90
└ correctness0.89
└ downstream usability0.92
└ efficiency0.92
└ intent fidelity0.85
└ style adherence0.94

Description

Build a manuscript-facing prototype schematic for the three selected Fig5 recombination events using the manifest from fig5-synteny-event-manifest.

Concept: The existing interval/color tracks are good for debugging but hard for readers. Make an SVbyEye/SyRI-like static schematic: chromosome/ideogram tracks for the involved haplotypes, highlighted source windows, and curved ribbons/splines showing which donor haplotype segments map into the child/recombinant haplotype. Use labels and geometry, not many colors, to communicate the event.

Required views:

  1. Full/context view: fig5_synteny_recombination_full.svg and, if possible, .pdf.
    • Three rows, one per event: PAR1 positive control, PHR candidate 1, PHR candidate 2.
    • For each event, draw the child/recombinant haplotype and the relevant parental/source haplotype chromosomes or chromosome arms. The user expects roughly three chromosome tracks per event; if the manifest requires a fourth because a side fragment comes from another chromosome, include it explicitly and keep it visually secondary.
    • Show chromosome context using G-banded or ideogram-like chromosomes. First search locally for a cytoband/G-band resource. If none exists, use data/chm13.chrom.sizes for chromosome length context plus neutral ideogram bands, and clearly label this as schematic, not exact cytobands. If fetching a stable public cytoband file is easier and safe, record the URL/provenance in README, but do not block the prototype on exact G-bands.
    • Highlight subtelomeric source windows and draw flow ribbons from donor/source segments to child/query segments.
  2. Focus view: fig5_synteny_recombination_focus.svg and, if possible, .pdf.
    • Zoom into the actual event windows with the same event ordering.
    • Use native assembly coordinates from the manifest/selected segments; do not revert to local 0-500 kb offsets as the primary labels.
    • Use consistent physical scaling or explicit scale bars, so a 150 kb PAR1 block and a 40 kb autosomal block are not visually equated without context.

Implementation guidance:

  • A lightweight standard-library Python SVG renderer is acceptable and probably preferable. Do not assume matplotlib/pandas are installed. Reuse simple PDF-writing patterns from prior brainstorming scripts if needed; SVG alone is acceptable only if PDF conversion is unavailable and that limitation is documented.
  • Keep the palette restrained: B/W or gray chromosome tracks, one strong flow color for PAR1, one strong flow color for autosomal PHR primary donor, muted secondary/low-confidence flows. Avoid a 23-color chromosome legend.
  • Draw flows as ribbons/splines between actual segment positions, with labels for donor arm/haplotype and native coordinate windows. Make small side fragments visible but not dominant.
  • Use the manifest as the event authority. Do not reselect events from patches.tsv. Drawing geometry must come from strict primary-path selected_segments.tsv / conservative_segments.tsv provenance.

Required outputs under paper_prep/_brainstorming/fig5_synteny_recombination_schematic/:

  • fig5_synteny_recombination_full.svg and .pdf if feasible.
  • fig5_synteny_recombination_focus.svg and .pdf if feasible.
  • plot_synteny_recombination_schematic.py with a documented regeneration command.
  • Update README.md with how to inspect/regenerate the schematic and what coordinate/band source is used.

Constraints:

  • Do not edit submission/ or replace the manuscript Fig5.
  • Do not run heavy alignments on the head node. Use the manifest and existing strict path tables.
  • Do not claim event-level validation. PAR1 is a positive control; PHR events are candidates compatible with exchange.
  • Commit with project convention: feat: fig5-synteny-schematic-prototype (agent-NNN).

Validation:

  • Both full/context and focus SVGs exist.
  • PDFs exist, or README states why SVG-only was produced.
  • Three event rows are present and labels distinguish PAR1 positive control from candidate PHR events.
  • Coordinates shown are native genomic coordinates from the manifest, not local offsets.
  • Visual relies on tracks/ribbons/splines and labels rather than many chromosome colors.
  • The second PHR event matches the manifest and is not the misleading earlier PAN028 chr3q strict-path panel unless justified by the manifest.

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Required by

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