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CLI: Visualization

helix viz minimizers --input minimizers.json --save mins.png
helix viz minimizers --schema   # print schema + sample payload

Flags:

  • --save writes PNG/SVG/PDF.
  • --save-viz-spec overrides the .viz.json path.
  • --schema bypasses plotting and prints the JSON contract + sample payload.

All viz commands (minimizers, seed-chain, rna-dotplot, alignment-ribbon, distance-heatmap, motif-logo) mirror this interface and emit <image>.provenance.json.

Edit DAG visualizations

helix edit-dag viz --input dag.json --out dag.png \
  [--layout timeline|spring|...] [--min-prob 0.05] [--max-time 6]

Plots any helix.*.edit_dag.v* artifact (CRISPR, Prime, PCR) using the cinematic renderer. --layout controls node layering (timeline default), while --min-prob/--max-time filter cluttered graphs before drawing.

HTML reports

helix edit-dag report --input dag.json --out report.html --png dag.png

Produces a single-page HTML summary (dark theme) with:

  • Metrics (node/edge counts, entropy, max probability, top outcomes)
  • Embedded PNG (optional) or a placeholder if omitted
  • Provenance-friendly JSON links

Great for attaching to PRs or sharing with teammates.

Compare two DAGs

helix edit-dag compare --a dag_before.json --b dag_after.json --out compare.png \
  --label-a "baseline" --label-b "design-B" --min-prob 0.02 \
  --summary diff.json
  • Blue nodes/edges appear only in the first artifact; orange ones only in the second; white are shared.
  • Uses the same filtering knobs (--layout, --min-prob, --max-time) as viz/animate.
  • Optional --summary diff.json writes a JSON report (unique/shared nodes, terminal outcomes, top probabilities).
  • Ideal for CRISPR vs PCR overlays, control vs experimental runs, or before/after optimization.