bog-v2-slide-08 — workgraph

Metadata

Status	done
Assigned	`agent-767`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-06T00:34:51.442243827+00:00
Started	2026-05-06T00:39:33.001622860+00:00
Completed	2026-05-06T00:46:55.278560114+00:00
Tags	`bog-slide`, `bog-this-week`, `eval-scheduled`
Eval score	0.85
└ blocking impact	0.87
└ completeness	0.82
└ constraint fidelity	0.70
└ coordination overhead	0.92
└ correctness	0.88
└ downstream usability	0.88
└ efficiency	0.90
└ intent fidelity	0.84
└ style adherence	0.92

Description

SHARED CONTEXT — BoG-this-week slide fanout. Lead author: Erik Garrison. Co-author: Andrea Guarracino. ANCHOR: paper_prep/synthesis/ABSTRACT.md. SUBSTRATE: end-to-end-report/ (Andrea 14-chapter report) + paper_prep/synthesis/CROSSWALK.md. EXISTING V1 DECK: slides/20260204_Subtelomics_overview_EG.summary.md (slide-by-slide ChatGPT extract — 240 lines, easiest entry) + slides/20260204_Subtelomics_overview_EG.pdf. TALK SLOT: 15 min. TOTAL SLIDES: 15. OUTPUT FILE: slides/v2/slide_NN_.md (NN = your slide number, slug short). FILE STRUCTURE (mandatory): ## Title (1 line) / ## Bullets (3-5, conference-style) / ## Primary figure (path if exists OR ggplot2/R generation script for any new annotation overlay; light R/ggplot2 work is OK inside agent worktree, no SBATCH) / ## Speaker notes (~150 words) / ## Time budget (target seconds matching the table) / ## Notes for synthesizer (cross-slide concerns, callbacks, what previous slide sets up). DO NOT modify v1 deck files. DO NOT touch other slide files in slides/v2/. Single output file. Single commit per task: "docs: BoG v2 slide NN — ".

THIS SLIDE: 08 — PCA colored by chromosome AND superpopulation (combine v1 slides 8 + 9 — same plot, two colorings, side-by-side or two-panel). v1 slide 8: PCA scatter colored by chromosome, p/q shape, dim 1 16.05% / dim 2 11.2%. v1 slide 9: same PCA, recolored by AFR/AMR/EAS/EUR/SAS — mixed clusters. CRITICAL CHECK: per CROSSWALK §3 C6, repo has MDS/PCoA + UMAP but NO explicit PCA. v1 may be MDS mislabeled as PCA. Verify by checking the data files referenced (hprcv2.1Mb.subtelo.full_mds.rds vs any pca file). RECOMMEND in Notes for synthesizer: (a) confirm IS PCA → keep, or (b) IS MDS → relabel "MDS / PCoA on Jaccard distance" and flag for abstract C6 wording fix. ADD callout: "population structure is real but secondary to arm-community structure". Cross-reference Hudson Fst out-of-Africa tree (CROSSWALK §1 ch.04 + ch.12: AFR/non-AFR Fst 0.10-0.15). Time budget: 70s.

SHARED CONTEXT — BoG-this-week slide fanout. Lead author: Erik Garrison. Co-author: Andrea Guarracino. ANCHOR: paper_prep/synthesis/ABSTRACT.md. SUBSTRATE: end-to-end-report/ (Andrea 14-chapter report) + paper_prep/synthesis/CROSSWALK.md. EXISTING V1 DECK: slides/20260204_Subtelomics_overview_EG.summary.md (slide-by-slide ChatGPT extract — 240 lines, easiest entry) + slides/20260204_Subtelomics_overview_EG.pdf. TALK SLOT: 15 min. TOTAL SLIDES: 15. OUTPUT FILE: slides/v2/slide_NN_<slug>.md (NN = your slide number, slug short). FILE STRUCTURE (mandatory): ## Title (1 line) / ## Bullets (3-5, conference-style) / ## Primary figure (path if exists OR ggplot2/R generation script for any new annotation overlay; light R/ggplot2 work is OK inside agent worktree, no SBATCH) / ## Speaker notes (~150 words) / ## Time budget (target seconds matching the table) / ## Notes for synthesizer (cross-slide concerns, callbacks, what previous slide sets up). DO NOT modify v1 deck files. DO NOT touch other slide files in slides/v2/. Single output file. Single commit per task: "docs: BoG v2 slide NN — <slug>".

THIS SLIDE: 08 — PCA colored by chromosome AND superpopulation (combine v1 slides 8 + 9 — same plot, two colorings, side-by-side or two-panel).
v1 slide 8: PCA scatter colored by chromosome, p/q shape, dim 1 16.05% / dim 2 11.2%. v1 slide 9: same PCA, recolored by AFR/AMR/EAS/EUR/SAS — mixed clusters.
CRITICAL CHECK: per CROSSWALK §3 C6, repo has MDS/PCoA + UMAP but NO explicit PCA. v1 may be MDS mislabeled as PCA. Verify by checking the data files referenced (hprcv2.1Mb.subtelo.full_mds.rds vs any *pca* file). RECOMMEND in Notes for synthesizer: (a) confirm IS PCA → keep, or (b) IS MDS → relabel "MDS / PCoA on Jaccard distance" and flag for abstract C6 wording fix.
ADD callout: "population structure is real but secondary to arm-community structure". Cross-reference Hudson Fst out-of-Africa tree (CROSSWALK §1 ch.04 + ch.12: AFR/non-AFR Fst 0.10-0.15). Time budget: 70s.

Depends on

done .assign-bog-v2-slide-08

Required by

Log

2026-05-06T00:34:51.418921095+00:00 Task paused
2026-05-06T00:37:42.482378016+00:00 Task published
2026-05-06T00:39:29.113279528+00:00 Lightweight assignment: agent=random-agent-3577bc75 (3577bc75), exec_mode=full, context_scope=task, reason=Documenter role with verify-against-code tradeoff is ideal for creating structured slide documentation with critical data file verification (PCA vs MDS check) and potential light figure annotation.
2026-05-06T00:39:33.001626116+00:00 Spawned by coordinator --executor claude --model opus
2026-05-06T00:39:48.608793872+00:00 Starting slide 08 — PCA combined chromosome + superpopulation
2026-05-06T00:45:59.888769664+00:00 Drafted slide_08_pca_chromosome_superpop.md combining v1 slides 8+9; flagged MDS/PCoA-vs-PCA mislabeling per CROSSWALK §3 C6 (cmdscale at line 556 of plot-similarity-subtelo.R, no *pca* file in HPRCv2 tree); included Hudson Fst secondary-structure callout
2026-05-06T00:46:44.064095285+00:00 Committed: f1d2478 — pushed to origin
2026-05-06T00:46:49.287664013+00:00 Validated: file has all 6 required sections (Title, Bullets, Primary figure, Speaker notes, Time budget, Notes for synthesizer); single output file; single commit; only my file staged
2026-05-06T00:46:55.278564692+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-06T00:50:42.191576004+00:00 PendingEval → Done (evaluator passed; downstream unblocks)