review-zoom-v7-slide09-community-mds-layout

Metadata

Status	done
Assigned	`agent-1123`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-07T19:42:55.090164984+00:00
Started	2026-05-07T19:46:55.432417198+00:00
Completed	2026-05-07T19:59:42.339810453+00:00
Tags	`review-zoom`, `review-zoom-v7`, `slide09`, `mds`, `communities`, `eval-scheduled`
Eval score	0.92
└ blocking impact	0.92
└ completeness	0.92
└ coordination overhead	0.91
└ correctness	0.93
└ downstream usability	0.94
└ efficiency	0.90
└ intent fidelity	0.88
└ style adherence	0.89

Description

Rebuild slide 09 so it uses the same visual layout/grammar as slide 08a, but labeled and colored by community. Erik says current slide 09 is only OK and wants the MDS, not PCA, with all communities labeled.\n\nGoal:\n- Produce a community-colored MDS scatter using the same layout style as slide 08a: same plot frame proportions, 1:1 aspect, comparable point styling, readable axes.\n- Label by community and color by community.\n- Avoid PCA unless included only as a background/source note; the slide should lead with MDS.\n\nImplementation guidance:\n- Locate the current MDS coordinate source and the existing v3 all-community label task outputs.\n- Use stable C1-C15 labels and community colors. If labels overlap, use ggrepel or a clear offset strategy.\n- Make labels readable at slide scale and use the same color scheme as the heatmaps/community slides where possible.\n- Include concise support text: communities were assigned from arm-level graph Jaccard distances, not from 3D/gene labels.\n\nDeliverables:\n- Reproducible script(s), README, rendered PNG/PDF under slides/v2-review-zoom/_revision_assets/v7/09_community_mds_layout/.\n- SLIDE_PATCH.md specifying replacement for slide 09 and any caption/notes.\n- Validation note that axes are 1:1, MDS is used, and all communities are labeled.\n\nDo not make final deck integration changes; leave that to review-zoom-v7-fanin-render.

Rebuild slide 09 so it uses the same visual layout/grammar as slide 08a, but labeled and colored by community. Erik says current slide 09 is only OK and wants the MDS, not PCA, with all communities labeled.\n\nGoal:\n- Produce a community-colored MDS scatter using the same layout style as slide 08a: same plot frame proportions, 1:1 aspect, comparable point styling, readable axes.\n- Label by community and color by community.\n- Avoid PCA unless included only as a background/source note; the slide should lead with MDS.\n\nImplementation guidance:\n- Locate the current MDS coordinate source and the existing v3 all-community label task outputs.\n- Use stable C1-C15 labels and community colors. If labels overlap, use ggrepel or a clear offset strategy.\n- Make labels readable at slide scale and use the same color scheme as the heatmaps/community slides where possible.\n- Include concise support text: communities were assigned from arm-level graph Jaccard distances, not from 3D/gene labels.\n\nDeliverables:\n- Reproducible script(s), README, rendered PNG/PDF under slides/v2-review-zoom/_revision_assets/v7/09_community_mds_layout/.\n- SLIDE_PATCH.md specifying replacement for slide 09 and any caption/notes.\n- Validation note that axes are 1:1, MDS is used, and all communities are labeled.\n\nDo not make final deck integration changes; leave that to review-zoom-v7-fanin-render.

Depends on

Required by

Log

2026-05-07T19:42:55.063049924+00:00 Task paused
2026-05-07T19:43:48.924942534+00:00 Task published
2026-05-07T19:46:55.432421446+00:00 Spawned by coordinator --executor codex --model gpt-5.5
2026-05-07T19:47:40.282279444+00:00 Starting implementation: inspecting slide 08a/09 assets, v3 community-label output, and available MDS coordinate sources.
2026-05-07T19:50:12.934362234+00:00 Found inputs: current slide 08a asset is 12x10 / 3600x3000 from plot-similarity-subtelo.R; MDS source is full_mds.rds; usable v3 all-community label output is v3/09_all_communities_1to1 (task input path name is stale).
2026-05-07T19:56:32.947215418+00:00 Validated: R renderer regenerated PNG/PDF; PNG is 3600x3000; validation_summary.tsv confirms MDS source, coord_fixed 1:1 axes, no PCA coordinates, and labels C1-C15.
2026-05-07T19:58:37.346648223+00:00 Committed: f946afc — pushed to remote branch wg/agent-1123/review-zoom-v7-slide09-community-mds-layout.
2026-05-07T19:59:42.339818619+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-07T20:03:42.427478808+00:00 PendingEval → Done (evaluator passed; downstream unblocks)