review-zoom-v4-slide10a-xaxis-orientation-fix

Metadata

Status	done
Assigned	`agent-1050`
Agent identity	`f51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e`
Created	2026-05-07T13:40:03.184817912+00:00
Started	2026-05-07T13:41:53.949895356+00:00
Completed	2026-05-07T13:58:17.381200750+00:00
Tags	`bog-this-week`, `bog-deck`, `review-zoom`, `review-zoom-v4`, `render`, `eval-scheduled`
Eval score	0.94
└ blocking impact	0.89
└ completeness	0.96
└ constraint fidelity	0.70
└ coordination overhead	0.93
└ correctness	0.95
└ downstream usability	0.95
└ efficiency	0.89
└ intent fidelity	0.88
└ style adherence	0.94

Description

Focused v4 correction for Erik's latest review: slide 10a still appears flipped/inverted on the X axis.

Goal: fix only slide 10a's displayed X-axis orientation in the review zoom deck, then render a v4 deck. Do not broad-redesign the deck.

Critical user feedback:

Erik says v3 slide 10a is still apparently flipped / inverted on the X axis. Treat this as the acceptance target; the previous v3 task only asserted analytical row/column name equality and missed the visual orientation problem.

Required investigation:

Inspect current v3 slide 10a asset and generator: slides/v2-review-zoom/_revision_assets/v3/10a_axis_box_fix/.
Inspect original figure generator: paper_prep/figures/fig3/figure_fig3.R, especially panel A display transform.
Inspect v2 redesign generator if useful: slides/v2-review-zoom/_revision_assets/hic_visual_redesign/make_hic_visual_redesign.R.
Do not accept matrix symmetry or identical row/column vectors as sufficient validation; a symmetric matrix can hide an inverted displayed X axis.

Implementation requirements:

Regenerate a corrected slide-10a asset under slides/v2-review-zoom/_revision_assets/v4/10a_xaxis_orientation/.
Explicitly address the visual X-axis orientation. If the current v3 asset is mirrored left/right, reverse the displayed column order and recompute boxes/labels in the displayed coordinate system.
Add unambiguous corner/axis labels or a small orientation audit so the viewer can tell which side of the X axis is first/last; avoid vague labels like only "community ordered" if that hides inversion.
Preserve the HG002 Pore-C matrix source, B/W statistic, p-value, and sequence-community interpretation unless the audit proves one is wrong.
Produce orientation_audit.tsv documenting row order, displayed column order, whether the v3 X axis was mirrored, and the corrected policy.
Update the Typst deck source to use the corrected asset for slide 10a only.
Render slides/v2-review-zoom/BoG_2026_review_zoom_v4.pdf and page PNGs. Preserve v1/v2/v3 PDFs.
Write slides/v2-review-zoom/REVISION_NOTES_V4.md explaining exactly what was changed and why v3 validation missed it.

Validation:

v4 PDF renders successfully and page count remains plausible.
Slide/page 10a renders nonblank.
orientation_audit.tsv exists and explicitly states the corrected X-axis policy.
The corrected asset is not just a copy of the v3 asset.
git diff --check passes.
No stale .wg-worktrees absolute paths are embedded under slides/v2-review-zoom.

Focused v4 correction for Erik's latest review: slide 10a still appears flipped/inverted on the X axis.

Goal: fix only slide 10a's displayed X-axis orientation in the review zoom deck, then render a v4 deck. Do not broad-redesign the deck.

Critical user feedback:
- Erik says v3 slide 10a is still apparently flipped / inverted on the X axis. Treat this as the acceptance target; the previous v3 task only asserted analytical row/column name equality and missed the visual orientation problem.

Required investigation:
- Inspect current v3 slide 10a asset and generator: `slides/v2-review-zoom/_revision_assets/v3/10a_axis_box_fix/`.
- Inspect original figure generator: `paper_prep/figures/fig3/figure_fig3.R`, especially panel A display transform.
- Inspect v2 redesign generator if useful: `slides/v2-review-zoom/_revision_assets/hic_visual_redesign/make_hic_visual_redesign.R`.
- Do not accept matrix symmetry or identical row/column vectors as sufficient validation; a symmetric matrix can hide an inverted displayed X axis.

Implementation requirements:
- Regenerate a corrected slide-10a asset under `slides/v2-review-zoom/_revision_assets/v4/10a_xaxis_orientation/`.
- Explicitly address the visual X-axis orientation. If the current v3 asset is mirrored left/right, reverse the displayed column order and recompute boxes/labels in the displayed coordinate system.
- Add unambiguous corner/axis labels or a small orientation audit so the viewer can tell which side of the X axis is first/last; avoid vague labels like only "community ordered" if that hides inversion.
- Preserve the HG002 Pore-C matrix source, B/W statistic, p-value, and sequence-community interpretation unless the audit proves one is wrong.
- Produce `orientation_audit.tsv` documenting row order, displayed column order, whether the v3 X axis was mirrored, and the corrected policy.
- Update the Typst deck source to use the corrected asset for slide 10a only.
- Render `slides/v2-review-zoom/BoG_2026_review_zoom_v4.pdf` and page PNGs. Preserve v1/v2/v3 PDFs.
- Write `slides/v2-review-zoom/REVISION_NOTES_V4.md` explaining exactly what was changed and why v3 validation missed it.

Validation:
- v4 PDF renders successfully and page count remains plausible.
- Slide/page 10a renders nonblank.
- `orientation_audit.tsv` exists and explicitly states the corrected X-axis policy.
- The corrected asset is not just a copy of the v3 asset.
- `git diff --check` passes.
- No stale `.wg-worktrees` absolute paths are embedded under `slides/v2-review-zoom`.

Depends on

Required by

done .flip-review-zoom-v4-slide10a-xaxis-orientation-fix

✉ Messages 2 messages (2 unread)

#1codex-parent2026-05-07T13:43:59.714682718+00:00read

Heads up: identify/pdftoppm are available at /home/erikg/micromamba/bin/identify and /home/erikg/micromamba/bin/pdftoppm if you need pixel/PDF validation; current bare PATH may not include micromamba. You can use PATH=/home/erikg/micromamba/bin:$PATH for those checks.

#2review-zoom-v4-slide10a-xaxis-orientation-fix2026-05-07T13:50:47.468014486+00:00read

Acknowledged — will prepend /home/erikg/micromamba/bin for identify/pdftoppm during PDF and pixel validation as needed.

Log

2026-05-07T13:40:03.160919650+00:00 Task paused
2026-05-07T13:40:05.510373578+00:00 Task published
2026-05-07T13:41:07.378661667+00:00 Lightweight assignment: agent=Careful Programmer (f5143935), exec_mode=full, context_scope=graph, reason=Correctness-critical slide repair with code edits, render checks, and audit notes fits a careful programming agent best.
2026-05-07T13:41:53.949899915+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-07T13:42:10.185172047+00:00 Starting v4 slide 10a X-axis orientation correction; no unread messages at start.
2026-05-07T13:42:26.798184026+00:00 FANOUT_DECISION: stay inline — focused slide-only correction with sequential inspect/generate/render/validate steps and overlapping file scope.
2026-05-07T13:50:26.647899628+00:00 Generated v4 slide 10a asset and orientation audit; v3 X-axis mirror is documented as rasterImage/as.raster transform issue, not row/column-name mismatch.
2026-05-07T13:55:39.609067349+00:00 Validated v4 render: Typst PDF 33 pages, page-20 PNG nonblank, orientation_audit.tsv states v3_x_axis_mirrored=TRUE and corrected X policy, v4 asset differs from v3, git diff --check passes, no .wg-worktrees paths under slides/v2-review-zoom.
2026-05-07T13:57:46.576240661+00:00 Committed: 642c234 — pushed to origin/wg/agent-1050/review-zoom-v4-slide10a-xaxis-orientation-fix
2026-05-07T13:58:17.381209377+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-07T14:03:50.027844827+00:00 PendingEval → Done (evaluator passed; downstream unblocks)