Graph Colorize Agent Skill

Graph Colorize — Color-code the Obsidian Graph View

You are rewriting $OBSIDIAN_VAULT_PATH/.obsidian/graph.json so Obsidian's graph view tints nodes by tag, folder, or visibility.

Obsidian stores graph settings in <vault>/.obsidian/graph.json. The colorGroups array is a list of {query, color} pairs; the first matching query wins per node. Queries use Obsidian's search syntax: tag:#foo, path:"concepts", file:foo, etc. Color is {"a": 1, "rgb": <packed-int>} where the int is (R << 16) | (G << 8) | B.

Before You Start

• Resolve config — follow the Config Resolution Protocol in llm-wiki/SKILL.md (inline @name override → walk up CWD for .env → ~/.obsidian-wiki/config → prompt setup). This gives OBSIDIAN_VAULT_PATH.
• Confirm $OBSIDIAN_VAULT_PATH/.obsidian/ exists. If it doesn't, the vault has never been opened in Obsidian — tell the user to open the vault once in Obsidian, then re-run.
• Warn the user if Obsidian is likely open: Obsidian overwrites graph.json on close. Tell them to close the vault first, or be ready to reload (Cmd/Ctrl+R) and not touch the graph settings until they reload.

Step 1: Pick a Mode

Infer the mode from the user's phrasing. If ambiguous, default to by-tag.

| User intent | Mode |

|---|---|

| "color by tag", "color my graph", "make it colorful" (default) | by-tag |

| "color by folder", "color by category", "color by directory" | by-category |

| "highlight visibility", "show internal/pii in graph", "visibility colors" | by-visibility |

| User provides explicit mapping (tag:#foo = red, or JSON blob) | custom |

| "combine tag and visibility" / "both" | combined (visibility first, then tag) |

Step 2: Build the colorGroups Array

Palette (10 distinct, colorblind-friendly colors)

Use in order. If more groups than colors, cycle and add a lightness shift by dividing brightness ~20% via a second pass — or just cap at 10 and tell the user the remaining tags share the "other" color.

| # | Hex | rgb (packed int) | Role |

|---|---|---|---|

| 0 | #4E79A7 | 5142951 | blue |

| 1 | #F28E2B | 15896107 | orange |

| 2 | #E15759 | 14767961 | red |

| 3 | #76B7B2 | 7780786 | teal |

| 4 | #59A14F | 5873999 | green |

| 5 | #EDC948 | 15583048 | yellow |

| 6 | #B07AA1 | 11565217 | purple |

| 7 | #FF9DA7 | 16751527 | pink |

| 8 | #9C755F | 10253663 | brown |

| 9 | #BAB0AC | 12234924 | gray |

Every color is wrapped as {"a": 1, "rgb": <int>}.

Mode: by-tag

• Glob $VAULT_PATH/**/*.md excluding _archives/, _raw/, .obsidian/, node_modules/, index.md, log.md, _insights.md.
• Parse frontmatter tags from each page. Count usage per tag.
• Drop visibility/* tags from the frequency list — they are reserved system tags, handled only in by-visibility or combined mode.
• Take the top 10 tags by usage. If there are fewer than 10 unique tags, use all of them.
• For each tag T at index i: emit {"query": "tag:#T", "color": palette[i]}.
• Optionally, append a final catch-all entry for untagged pages at the end: {"query": "-[\"tag\":]", "color": palette[9]} — skip if color slot 9 is already taken by a real tag.

Mode: by-category

Use the seven vault top-level folders in this fixed order so colors are stable across runs:

| Folder | Color index |

|---|---|

| concepts | 0 (blue) |

| entities | 1 (orange) |

| skills | 2 (red) |

| references | 3 (teal) |

| synthesis | 4 (green) |

| projects | 5 (yellow) |

| journal | 6 (purple) |

Emit one entry per folder that exists AND contains at least one .md file. Each entry is:

{"query": "path:\"<folder>\"", "color": {"a": 1, "rgb": <int>}}

Mode: by-visibility

Emit exactly three entries, in this order (first-match wins, so most restrictive comes first):

• visibility/pii → #E15759 (red, rgb 14767961)
• visibility/internal → #F28E2B (orange, rgb 15896107)
• visibility/public → #59A14F (green, rgb 5873999)

{"query": "tag:#visibility/pii", "color": {"a": 1, "rgb": 14767961}}

Pages with no visibility/ tag remain Obsidian's default color — do not add a catch-all.

Mode: combined

Emit by-visibility entries first, then by-tag entries. Visibility wins on conflict because it appears first in the list.

Mode: custom

If the user gave explicit mappings, honor them literally. Convert any hex they give (e.g. #FF00FF) to packed int using int(hex_without_hash, 16). Wrap each as {"a": 1, "rgb": <int>}.

Step 3: Merge into graph.json (Do Not Clobber)

• Read the existing $VAULT_PATH/.obsidian/graph.json. If it doesn't exist, start from this minimal default:

   {
     "collapse-filter": true,
     "search": "",
     "showTags": false,
     "showAttachments": false,
     "hideUnresolved": false,
     "showOrphans": true,
     "collapse-color-groups": false,
     "colorGroups": [],
     "collapse-display": true,
     "showArrow": false,
     "textFadeMultiplier": 0,
     "nodeSizeMultiplier": 1,
     "lineSizeMultiplier": 1,
     "collapse-forces": true,
     "centerStrength": 0.518713248970312,
     "repelStrength": 10,
     "linkStrength": 1,
     "linkDistance": 250,
     "scale": 1,
     "close": true
   }

• Back up first: copy the existing file to .obsidian/graph.json.backup-<YYYYMMDD-HHMM> before writing. If a backup from the same minute exists, reuse it — don't pile up duplicates.

• Replace only the colorGroups field with your new array. Leave every other field untouched. This preserves the user's zoom, physics, filter, search, and display preferences.

• Write the file back with the same JSON style as the original (usually compact single-line or 2-space indent — preserve what's there).

Step 4: Report and Log

Print a summary like:

Graph colorized → .obsidian/graph.json
  Mode:    by-tag
  Groups:  7 color assignments
  Palette: blue, orange, red, teal, green, yellow, purple
  Backup:  .obsidian/graph.json.backup-20260424-1432

Reload Obsidian (Cmd/Ctrl+R) to see the new colors.
If Obsidian is currently open, close it first OR reload immediately — Obsidian
overwrites graph.json on close and can erase these changes.

Append to $VAULT_PATH/log.md:

- [TIMESTAMP] GRAPH_COLORIZE mode=<mode> groups=<N> backup=graph.json.backup-<stamp>

Edge Cases

• No tags in vault in by-tag mode → fall back to by-category and tell the user.
• User wants to undo → restore from the latest graph.json.backup-* and note that in log.md.
• User wants to clear all color groups → set colorGroups: [], back up, log as GRAPH_COLORIZE mode=clear.
• .obsidian/ missing → the vault hasn't been opened in Obsidian yet. Tell the user to open it once, then re-run. Don't create .obsidian/ yourself — Obsidian populates many files there on first open.
• Query syntax gotchas: folder paths with spaces need quoting (path:"my folder"); tags with nested slashes work literally (tag:#visibility/internal); don't URL-encode.
• Obsidian open during edit: surface the risk — Obsidian reads graph.json at startup and rewrites it on close. If the user is editing live, tell them to close Obsidian first or run the reload (Cmd/Ctrl+R) immediately and avoid opening graph settings before they do.

Notes

• This is a pure config edit — no page content changes, no frontmatter writes.
• Re-running is safe: each run creates a new backup, only colorGroups is rewritten.
• If the user has manually curated color groups they want to keep, offer combined mode or ask before overwriting.
• The palette here matches wiki-export's graph.html community colors, so the Obsidian graph and the exported visualization look consistent.