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review-zoom-v5-07a-tree-community-heatmaps

Render 07a tree-then-community heatmap pair for review zoom v5

Metadata

Statusdone
Assignedagent-1060
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-05-07T15:12:35.280726834+00:00
Started2026-05-07T15:13:21.999108001+00:00
Completed2026-05-07T15:35:05.679490196+00:00
Tagsreview-zoom, review-zoom-v5, heatmap, community, slide07, eval-scheduled
Eval score0.89
└ blocking impact0.90
└ completeness0.95
└ constraint fidelity0.70
└ coordination overhead0.88
└ correctness0.88
└ downstream usability0.93
└ efficiency0.82
└ intent fidelity0.82
└ style adherence0.84

Description

Render a two-step heatmap story for review-zoom v5: first the tree-ordered similarity heatmap with the tree to the side, then the same matrix sorted/grouped by community without the tree.

User intent:

  • Erik liked the heatmap sorted by community.
  • In the talk, show the NJ/tree-ordered heatmap first, then a community-sorted version to make the grouping obvious.
  • The community-sorted version should be the same underlying rendering/matrix style, but with no NJ/tree and with boxes/bands for community groupings.
  • This should complement the existing slide 07a/07b story, not redesign the whole deck.

Starting points:

  • Existing crisp/tree asset: slides/v2-review-zoom/_revision_assets/v3/07a_crisp_aligned/
  • Existing prior community/tree asset: slides/v2-review-zoom/_revision_assets/07a_heatmap_tree_pq/
  • Existing current deck Typst/assets: slides/v2-review-zoom/_typst/
  • Community assignments: paper_prep/figures/fig1/architecture_per_arm.tsv and HPRCv2 arm community tables if needed.

Implementation requirements:

  • Produce two slide-ready assets under slides/v2-review-zoom/_revision_assets/v5/07a_tree_then_community_heatmap/:
    1. 07a_tree_ordered_heatmap.png/.pdf: matrix ordered by the current tree/order, with the tree shown on the side and row/column labels aligned. Prefer the crisp v3 implementation if it is the best starting point.
    2. 07a_community_ordered_heatmap.png/.pdf: same matrix/data scale and visual style, sorted by C1, C2, ... community grouping, no tree, with community boxes/bands along the axes.
  • Keep p/q arm labeling legible. If practical, preserve the earlier red/blue p/q label cue, but do not let it clutter the community view.
  • Make the community grouping visually clear enough that v5 can show these as two sequential slides: "tree reveals structure" then "communities summarize it."
  • Include an audit TSV documenting the matrix source, tree/order source, community order, arm labels included/missing, and whether any arms have community assignment but no called CHM13 PHR interval. Do not imply all community-assigned arms have called CHM13 PHR intervals.
  • Use stable dimensions and high-resolution raster output suitable for Typst slides.

Deliverables:

  • slides/v2-review-zoom/_revision_assets/v5/07a_tree_then_community_heatmap/README.md
  • slides/v2-review-zoom/_revision_assets/v5/07a_tree_then_community_heatmap/make_07a_tree_then_community_heatmap.R or equivalent reproducible script
  • slides/v2-review-zoom/_revision_assets/v5/07a_tree_then_community_heatmap/07a_tree_ordered_heatmap.png
  • slides/v2-review-zoom/_revision_assets/v5/07a_tree_then_community_heatmap/07a_community_ordered_heatmap.png
  • Matching .pdf assets and audit/order TSVs

Validation

  • Both PNG and PDF assets exist and are nonblank.
  • Tree-ordered asset has a side tree and aligned rows/columns.
  • Community-ordered asset has no side tree and clearly shows community boxes/bands ordered C1..C15 or documented subset order.
  • README explains how these two assets should be sequenced in v5.
  • Audit TSV records matrix source, tree/order source, community mapping, and arm inclusion/missing status.
  • git diff --check passes.

Depends on

Required by

✉ Messages 2 messages (2 unread)

  1. #1user2026-05-07T15:14:28.998671801+00:00read
    Erik correction for Slide 07a assets: adjust both output heatmaps so chromosome x/y labels are visibly larger, roughly 1.5x the previous/current label size. This applies to both the tree/UPGMA-ordered heatmap and the community-sorted heatmap. Keep the heatmap coloring/color scale/palette the same across both assets and consistent with the current 07a heatmap style; do not change colors while making labels larger. The community-sorted panel should still have no tree and should show community grouping boxes/bands. Please document the label-size/color-scale policy in the README/audit.
  2. #2review-zoom-v5-07a-tree-community-heatmaps2026-05-07T15:21:57.934069646+00:00read
    Acknowledged — I will enlarge chromosome x/y labels by about 1.5x in both heatmaps, keep the shared similarity palette unchanged, preserve no-tree community grouping bands, and document the label-size/color-scale policy in the README and audit.

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