← graph

review-zoom-v5-pggb-gfalook-2d-render

Add main-component PGGB graph visualization to review zoom v5

Metadata

Statusdone
Assignedagent-1084
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-05-07T15:58:21.570129390+00:00
Started2026-05-07T16:38:10.441510904+00:00
Completed2026-05-07T16:58:13.670893677+00:00
Tagsreview-zoom, review-zoom-v5, pggb, methods, graph-viz, odgi, eval-scheduled, gfalook
Eval score0.90
└ blocking impact0.95
└ completeness0.87
└ constraint fidelity0.40
└ coordination overhead0.90
└ correctness0.88
└ downstream usability0.91
└ efficiency0.95
└ intent fidelity0.77
└ style adherence0.89

Description

Use the existing ODGI/PGGB layout artifacts to put a graph visualization into the review-zoom v5 presentation.

User intent:

  • The PGGB graph already has layout/render artifacts; use an existing rendered PNG if it is slide-usable after cropping/rescaling.
  • If the existing full-graph PNG is too awkward, render the main graph component only so the visual is cleaner.
  • gfalook is acceptable if it gives a better image, but ODGI is preferred because the layout already exists.
  • Heavy render/layout/subgraph attempts must run via SLURM on the tux nodes, not on the head node. The tux partition has 96-core nodes visible via sinfo (tux05-tux09 observed idle at task creation).

Primary graph/layout inputs:

  • ODGI graph: /moosefs/guarracino/HPRCv2/PHR_III/pggb/hprcv2.1Mb.telo_trimmed.p95.id95/hprcv2.1Mb.telo_trimmed.p95.id95.fa.gz.6e0e250.11fba48.645f51d.smooth.final.og (~10.3 GB)
  • GFA graph, if needed for gfalook: /moosefs/guarracino/HPRCv2/PHR_III/pggb/hprcv2.1Mb.telo_trimmed.p95.id95/hprcv2.1Mb.telo_trimmed.p95.id95.fa.gz.6e0e250.11fba48.645f51d.smooth.final.gfa (~5.9 GB)
  • Existing ODGI layout coordinates: /moosefs/guarracino/HPRCv2/PHR_III/pggb/hprcv2.1Mb.telo_trimmed.p95.id95/hprcv2.1Mb.telo_trimmed.p95.id95.fa.gz.6e0e250.11fba48.645f51d.smooth.final.og.lay and .og.lay.tsv
  • Existing PNGs:
    • *.smooth.final.og.lay.draw.png is 167 x 1000 and likely too small/narrow for slides.
    • *.smooth.final.og.viz_multiqc.png is 1968 x 157164 and likely too tall/raw for slides.

Known component structure from .og.lay.tsv:

  • component 8: 727,156 layout nodes (largest/main component)
  • component 10: 133,896 layout nodes
  • component 9: 94,384 layout nodes
  • components 0-7: 2 layout nodes each

Implementation guidance:

  • First inspect existing PNGs. If a cropped/rescaled existing rendering gives a good slide image, use it and document the crop.
  • Prefer rendering the main component only if the full graph is unreadable. Use component 8 from the existing layout TSV as the main-component target unless direct graph-component tooling proves a different component label is needed.
  • Practical main-component route: derive node IDs for component 8 from .og.lay.tsv, extract those nodes from the ODGI graph with odgi extract --node-list ... --optimize, then either reuse/filter the layout coordinates or rerun a bounded layout for the extracted component.
  • Use ODGI commands where possible: odgi draw -i graph.og -c layout.lay -p output.png -s output.svg ...; odgi extract; odgi layout only if needed.
  • gfalook may be used if it gives a cleaner main-component or full-graph render, but it is not required.
  • For heavy work, create and submit an sbatch script, e.g. sbatch -p tux -c 96 --mem ... render_pggb_graph.slurm.sh. Use -t 96 or an appropriate thread count inside ODGI/gfalook. Do not run the full graph extraction/layout/render interactively on the head node.
  • Lightweight inspection, cropping/resizing, and Typst edits may run locally.
  • Write all new assets under slides/v2-review-zoom/_revision_assets/v5/pggb_graph_odgi/; do not overwrite canonical PGGB outputs under /moosefs/guarracino.
  • Make one slide-ready PNG for the deck, plus SVG if practical. Prefer a 16:9-ish composition rather than a giant full-height strip.
  • Add the graph visualization to the review-zoom v5 presentation after review-zoom-v5-phr-jaccard-method-slide has added the methods slide. Use it on that slide if it improves readability; otherwise add a short adjacent visual slide.
  • Label the image clearly as full graph, main component, crop, or subset.

Deliverables:

  • slides/v2-review-zoom/_revision_assets/v5/pggb_graph_odgi/README.md
  • slides/v2-review-zoom/_revision_assets/v5/pggb_graph_odgi/render_pggb_odgi_draw.sh or equivalent reproducible local wrapper
  • slides/v2-review-zoom/_revision_assets/v5/pggb_graph_odgi/render_pggb_graph.slurm.sh if any heavy render/extract/layout job is submitted
  • slides/v2-review-zoom/_revision_assets/v5/pggb_graph_odgi/pggb_graph_2d.png
  • Optional matching pggb_graph_2d.svg
  • slides/v2-review-zoom/_revision_assets/v5/pggb_graph_odgi/render_log.tsv or similar audit with exact command, SLURM job ID if used, graph/layout/png source, dimensions, and full-graph vs main-component/crop/subset status
  • Updated review-zoom v5 PDF and REVISION_NOTES_V5.md

Validation:

  • Output PNG exists, is nonblank, and has slide-usable dimensions/composition.
  • If heavy extraction/layout/rendering was needed, it ran through SLURM on tux, not on the head node.
  • The visualization is inserted into the v5 presentation.
  • README records whether the shown image is full graph, main component, crop, or subset.
  • README records exact source graph/layout/PNG files and ODGI/gfalook command(s) or crop command(s).
  • v5 PDF rerenders successfully after insertion.
  • REVISION_NOTES_V5.md records the PGGB graph visualization asset.
  • git diff --check passes.

Depends on

Required by

Log