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review-zoom-v6-dipc-validation-slides

Render review zoom v6 with Dip-C validation plots

Metadata

Statusdone
Assignedagent-1092
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-05-07T17:56:40.326065257+00:00
Started2026-05-07T17:57:25.274786138+00:00
Completed2026-05-07T18:21:59.404182096+00:00
Tagsreview-zoom, review-zoom-v6, dipc, sperm, 3d-validation, slides, eval-scheduled
Eval score0.95
└ blocking impact0.96
└ completeness0.95
└ constraint fidelity0.40
└ coordination overhead0.94
└ correctness0.96
└ downstream usability0.97
└ efficiency0.91
└ intent fidelity0.89
└ style adherence0.95

Description

Create review-zoom v6 by adding a concise Dip-C/sperm 3D validation section using the existing rendered outputs from end-to-end-report/report/06_dipc_validation.md and paper_prep/surveys/SURVEY_06_dipc_validation.md.

User intent:

  • Grab useful plots from the Dip-C validation report and drop them into the slides.
  • Use v6 as the new iteration.
  • Prefer already-rendered plots where they exist; do not re-run heavy 3D analyses unless absolutely needed.

Current finding / asset status:

  • The report Markdown itself has no embedded image links; it is prose/tables plus output paths.
  • Rendered PDFs already exist under /moosefs/guarracino/HPRCv2/dipc_t2t/... and should be used directly or converted to slide PNGs.
  • Existing slide asset slides/v2-review-zoom/_revision_assets/v3/11_wb_labels/slide11_explicit_distance_labels_candidate.png already summarizes C-community vs S_all W/B for GM12878 and sperm and may be reused or refreshed.

Primary existing rendered plots to stage/convert:

  • GM12878 Dip-C Mantel scatter: /moosefs/guarracino/HPRCv2/dipc_t2t/output_q0_XX/community_enrichment_k50/gm12878_mantel_scatter.pdf
  • GM12878 radial by community: /moosefs/guarracino/HPRCv2/dipc_t2t/output_q0_XX/community_enrichment_k50/gm12878_radial_community.pdf
  • Sperm Mantel scatter: /moosefs/guarracino/HPRCv2/dipc_t2t/sperm/enrichment_corrected/sperm_all20_mantel_scatter.pdf
  • Sperm radial by community: /moosefs/guarracino/HPRCv2/dipc_t2t/sperm/enrichment_corrected/sperm_all20_radial_community.pdf
  • Sperm shared/unshared overlay: /moosefs/guarracino/HPRCv2/dipc_t2t/sperm/overlay_plots/sperm_all20.by_arm-type.arm.pdf /moosefs/guarracino/HPRCv2/dipc_t2t/sperm/overlay_plots/sperm_all20.by_arm-type.per-cell.pdf
  • Optional PBMC reference only if useful: /moosefs/guarracino/HPRCv2/dipc_t2t/pbmc_hg19/enrichment_corrected/pbmc_mantel_scatter.pdf /moosefs/guarracino/HPRCv2/dipc_t2t/pbmc_hg19/enrichment_corrected/pbmc_radial_community.pdf

Primary TSV sources for any light recomposition/new summary plots:

  • GM12878 summary/per-cell/community-free: /moosefs/guarracino/HPRCv2/dipc_t2t/output_q0_XX/community_enrichment_k50/gm12878_summary.tsv /moosefs/guarracino/HPRCv2/dipc_t2t/output_q0_XX/community_enrichment_k50/gm12878_per_cell.tsv /moosefs/guarracino/HPRCv2/dipc_t2t/output_q0_XX/community_enrichment_k50/gm12878_community_free_per_cell.tsv /moosefs/guarracino/HPRCv2/dipc_t2t/output_q0_XX/community_enrichment_k50/gm12878_community_free_arm.tsv
  • Sperm summary/per-cell/community-free: /moosefs/guarracino/HPRCv2/dipc_t2t/sperm/enrichment_corrected/sperm_all20_summary.tsv /moosefs/guarracino/HPRCv2/dipc_t2t/sperm/enrichment_corrected/sperm_all20_per_cell.tsv /moosefs/guarracino/HPRCv2/dipc_t2t/sperm/enrichment_corrected/sperm_all20_community_free_per_cell.tsv /moosefs/guarracino/HPRCv2/dipc_t2t/sperm/enrichment_corrected/sperm_all20_community_free_arm.tsv
  • S_all / 500kb negative-control rows are described in the survey; locate and use the exact TSVs rather than guessing.

Slide goals:

  • Add 2-4 slides to v6, not a broad redesign.
  • Emphasize single-cell validation of the sequence-community story:
    1. GM12878 Dip-C: W/B=0.931, 6.9% closer; Fisher p=2.4e-05; Mantel rho=0.296, p=0.002.
    2. Sperm scHi-C: W/B=0.401, 60% closer; Fisher p=3.9e-51; Mantel rho=0.202, p=0.023.
    3. Negative control: non-sharing S_all arms are farther apart, GM12878 S_all W/B=1.106 and sperm S_all W/B=1.397; 0/16 GM12878 and 1/20 sperm cells below 1.
    4. Community-free per-cell similarity/proximity rho: GM12878 median rho=0.093, 15/16 positive; sperm median rho=0.029, 15/20 positive. Mention sperm arm-level pooled rho caveat if plotted.
  • Use existing report/survey language, but keep slide text short and readable.

Implementation guidance:

  • Start from the current v5 deck on main: slides/v2-review-zoom/BoG_2026_review_zoom_v5.pdf slides/v2-review-zoom/_typst/zoom_review_deck.typ
  • Write new assets under slides/v2-review-zoom/_revision_assets/v6/dipc_validation/.
  • Convert/stage PDFs to PNGs with reproducible commands; keep source PDFs or symlink/copy as appropriate for reproducibility in the repo commit.
  • If an existing PDF is too raw for slides, make a light recomposed plot from TSVs rather than rerunning the 3D analysis pipeline.
  • Good v6 slide candidates:
    • One slide with GM12878 + sperm Mantel/radial existing panels as a 2x2 or two sequential slides.
    • One high-signal W/B negative-control slide, reusing/refining v3/11_wb_labels if appropriate.
    • One per-cell community-free rho distribution slide if it is quick and clean from TSVs.
  • Do not overstate PBMC; report says PBMC community-free is unavailable and community-based PHR-coordinate PBMC is not foregrounded.
  • Update REVISION_NOTES_V6.md with exact sources and whether each slide used existing PDFs or generated new summary assets.

Deliverables:

  • slides/v2-review-zoom/BoG_2026_review_zoom_v6.pdf
  • slides/v2-review-zoom/REVISION_NOTES_V6.md
  • slides/v2-review-zoom/_revision_assets/v6/dipc_validation/README.md
  • Reproducible staging/conversion/plot script(s) under slides/v2-review-zoom/_revision_assets/v6/dipc_validation/
  • Slide-ready PNG/PDF assets under slides/v2-review-zoom/_revision_assets/v6/dipc_validation/
  • Page PNG exports for the new/changed v6 slides and nearby context.

Validation:

  • v6 PDF renders successfully.
  • New Dip-C/sperm slides use existing rendered plots where possible and document which ones were reused.
  • Any newly generated summary plots are built only from the listed TSVs and are reproducible.
  • New slides include the core GM12878, sperm, and S_all negative-control numbers with correct signs/directions.
  • Slides do not imply PBMC community-free exists.
  • Page PNG exports for new slides are nonblank and readable at 1920x1080.
  • REVISION_NOTES_V6.md and the asset README record exact sources.
  • git diff --check passes.
  • No stale .wg-worktrees absolute paths are embedded under slides/v2-review-zoom.

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