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figure-1-landscape-communities

Figure 1: subtelomeric landscape and arm-level communities

Metadata

Statusdone
Assignedagent-701
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-05-05T04:49:12.039779493+00:00
Started2026-05-05T05:37:36.463900030+00:00
Completed2026-05-05T05:57:00.909788917+00:00
Tagspaper-prep,figure, eval-scheduled
Eval score0.89
└ blocking impact0.95
└ completeness0.95
└ constraint fidelity0.85
└ coordination overhead0.90
└ correctness0.85
└ downstream usability0.90
└ efficiency0.85
└ intent fidelity0.88
└ style adherence0.90

Description

Description

Produce Main Fig 1 (4 panels) of the manuscript per paper_prep/synthesis/MANUSCRIPT_SKELETON.md. Implement directly — do not decompose further.

File scope

  • paper_prep/figures/fig1/figure_fig1.{pdf,png}
  • paper_prep/figures/fig1/figure_fig1.{R,py}
  • paper_prep/figures/fig1/caption.md
  • paper_prep/figures/fig1/sources.tsv

Figure spec (excerpt from MANUSCRIPT_SKELETON.md §Figure 1)

Figure 1 — Population-scale subtelomeric communities (the landscape)

Caption (preliminary). Inter-chromosomal subtelomeric sharing partitions 41 chromosome arms into 15 communities. (a) Genome-wide identity heatmap across 465 haplotypes shows discrete blocks of telomere-anchored shared sequence. (b) Number of chromosomes sharing each subtelomeric position with PHR-call overlay. (c) 41 × 41 arm-level distance heatmap with Leiden 15-community blocks annotated; UPGMA dendrogram on top (12/15 agreement). (d) Three architecture categories (homogeneous 8/41, polymorphic 34/41, fully interchangeable 7/41) annotated on a per-arm bar.

PanelContentStatusSource
1aGenome-wide stacked identity heatmap, 465 haplotypes × 24 chromosomesREADYp_genome_wide_identity_heatmap.pdf (or _no_inset.pdf) — SURVEY_FIG_inv §1
1bGenome-wide n-chromosomes-sharing heatmap with PHR BED overlayREADYp_genome_wide_numchrom_heatmap.pdf — SURVEY_FIG_inv §1
1c41×41 arm-level Jaccard heatmap with Leiden+UPGMA annotationGENERATEhprcv2.1Mb.subtelo.arm_dist_matrix.tsv + arm-leiden-k15.assignments.tsv — SURVEY_01 §1.8, §3
1dPer-arm architecture-category bar (homogeneous / polymorphic / fully interchangeable)GENERATEcross_arm_affinity_sequences.tsv + per-arm cross-arm rate — SURVEY_04 §1.11

Validation

  • All 4 panels addressed; each row in sources.tsv with status READY/GENERATE
  • Caption ≤ 200 words and cites at least 2 metrics with source TSV paths
  • PDF + PNG produced (PNG for talk re-use)
  • If a panel is blocked by a missing file, add a flag in WORK_DECOMPOSITION.md ## Gaps rather than running new wet-lab/large new computational analyses (architect guardrail)

Inputs to read first

  • paper_prep/synthesis/MANUSCRIPT_SKELETON.md (full skeleton)
  • paper_prep/surveys/SURVEY_01_pipeline.md, SURVEY_04_heterogeneity.md, SURVEY_FIG_inventory.md

Depends on

Required by

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