diagram

Diagram

Use nong for implemented scientific diagram rendering. Nong.Toolkit.Net routes to the CLI; do not recreate diagram rendering logic in scripts or temporary projects.

Nong CLI Preflight

Read ../../.claude/references/nong-cli-preflight.md before the first Nong CLI command in a session. Confirm the nong CLI is installed and the diagram command group.

Modular: nong diagram routes to the standalone Angri450.Nong.Tool.Diagram dotnet tool. First use auto-installs. Command surface unchanged.

Implemented Commands

nong diagram flowchart <spec.json> -o <out.png> [--json]
nong diagram network <spec.json> -o <out.png> [--json]
nong diagram tree <tree.nwk|tree.txt|spec.json> -o <out.png> [--json]

Dispatch

1. For process, workflow, protocol, or pipeline diagrams, prepare a flowchart JSON spec and run nong diagram flowchart.
2. For relationship, mechanism, interaction, or network diagrams, prepare a network JSON spec and run nong diagram network.
3. For phylogenetic trees, use Newick text (.nwk or .txt) or a tree JSON spec and run nong diagram tree.
4. Read artifacts.png from JSON output for the generated image path.
5. For Bioicons listing/search, use the icons skill.

Contracts

Flowchart JSON:

{
  "type": "flowchart",
  "title": "Workflow",
  "nodes": [
    { "id": "sample", "label": "Sample" },
    { "id": "dna", "label": "DNA extraction" }
  ],
  "edges": [
    { "from": "sample", "to": "dna" }
  ]
}

Network JSON:

{
  "nodes": [
    { "id": "A", "label": "Gene A" },
    { "id": "B", "label": "Gene B" }
  ],
  "edges": [
    { "from": "A", "to": "B", "label": "activates" }
  ],
  "title": "Interaction network"
}

Tree Newick:

((A:0.1,B:0.2):0.3,C:0.4);

Tree JSON:

{
  "type": "tree",
  "title": "Phylogeny",
  "newick": "((A:0.1,B:0.2):0.3,C:0.4);",
  "radial": false
}

Always use --json for generated diagrams. Treat status: "error" as failed and fix the spec before retrying.

Optional Visual QA

After generating a PNG, you may suggest:

nong ocr analyze-image tree.png -o tree.analysis --json

This is structural image QA for dimensions, blankness, whitespace, and content regions. It is not OCR, text recognition, or semantic understanding of the diagram.