Agent skill

Graph Colorize

by Ar9av in Ar9av/obsidian-wiki

Configure Obsidian graph colors by tag, folder, category, or visibility by updating .obsidian/graph.json.

MITAuto-check: notesKnowledge Management

Install Graph Colorize

skills CLI
$ npx skills add Ar9av/obsidian-wiki --skill graph-colorize -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install Ar9av/obsidian-wiki graph-colorize --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/Ar9av/obsidian-wiki.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.skills/graph-colorize .claude/skills/graph-colorize && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
graph-colorize
GitHub stars
3.5k
Token cost
~2k tokens
SKILL.md length
909 words
Files
1
Skills in repo
39
Repo updated
First seen
Licence
MIT

At a glance

Configure Obsidian graph colors by tag, folder, category, or visibility by updating .obsidian/graph.json.

  • Works in 4 steps: Pick a Mode → Build the colorGroups Array → Merge into graph.json (Do Not Clobber) → …
  • Graph colorization
  • SKILL.md covers Before You Start, Step 1: Pick a Mode, Step 2: Build the colorGroups… and Step 3: Merge into graph.json…, plus 3 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Graph Colorize is an agent skill from Ar9av/obsidian-wiki. Configure Obsidian graph colors by tag, folder, category, or visibility by updating .obsidian/graph.json. Use for graph colorization; preserve other graph settings and back up before changes.

Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Knowledge Management. It works with Obsidian. The repository describes itself as: Framework for AI agents to build and maintain a digital brain through Obsidian wiki | Memory System for Agents. The licence is MIT.

When your agent uses it

  • Graph colorization
  • Preserve other graph settings and back up before changes

Example prompts

  • “/graph-colorize”

Workflow steps

4 steps, taken from the step headings in SKILL.md.

  1. Pick a Mode
  2. Build the colorGroups Array
  3. Merge into graph.json (Do Not Clobber)
  4. Report and Log

What it can do on your machine

Read from SKILL.md and the folder at commit 709727e. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are json).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Graph Colorize loads about 2k tokens when it runs. Until then it costs about 52 tokens; SKILL.md has 909 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~52
When it runs · the whole SKILL.md, loaded when a task matches
~2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NoteMentions a .env fileSKILL.md:15
    line `@name` override → walk up CWD for `.env` → global config → prompt setup). This gives `OBSIDIAN_VAULT_PATH`.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from Ar9av/obsidian-wiki at commit 709727e, republished under its MIT licence (© Ar9av). 909 words, ~2,005 tokens.

Download SKILL.mdSave it as .claude/skills/graph-colorize/SKILL.md (or your agent's skills folder).
name
graph-colorize
description
Configure Obsidian graph colors by tag, folder, category, or visibility by updating .obsidian/graph.json. Use for graph colorization; preserve other graph settings and back up before changes.

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

  1. Resolve config — follow the Config Resolution Protocol in llm-wiki/SKILL.md (inline @name override → walk up CWD for .env → global config → prompt setup). This gives OBSIDIAN_VAULT_PATH.
  2. 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.
  3. 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 intentMode
"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.

#Hexrgb (packed int)Role
0#4E79A75142951blue
1#F28E2B15896107orange
2#E1575914767961red
3#76B7B27780786teal
4#59A14F5873999green
5#EDC94815583048yellow
6#B07AA111565217purple
7#FF9DA716751527pink
8#9C755F10253663brown
9#BAB0AC12234924gray

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

Mode: by-tag
  1. Glob $VAULT_PATH/**/*.md excluding _archives/, _raw/, .obsidian/, node_modules/, index.md, log.md, _insights.md.
  2. Parse frontmatter tags from each page. Count usage per tag.
  3. Drop visibility/* tags from the frequency list — they are reserved system tags, handled only in by-visibility or combined mode.
  4. Take the top 10 tags by usage. If there are fewer than 10 unique tags, use all of them.
  5. For each tag T at index i: emit {"query": "tag:#T", "color": palette[i]}.
  6. 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:

FolderColor index
concepts0 (blue)
entities1 (orange)
skills2 (red)
references3 (teal)
synthesis4 (green)
projects5 (yellow)
journal6 (purple)

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

json
{"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):

  1. visibility/pii → #E15759 (red, rgb 14767961)
  2. visibility/internal → #F28E2B (orange, rgb 15896107)
  3. visibility/public → #59A14F (green, rgb 5873999)
json
{"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.

Show full SKILL.md (382 more words)Show less
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)

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

    json
    {
      "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
    }
  2. 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.

  3. 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.

  4. 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.

© Ar9av, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in .skills/graph-colorize of Ar9av/obsidian-wiki.

Open the folder on GitHubat commit 709727e

Compare with similar skills

Graph Colorize next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Graph Colorize compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Graph Colorize this skillAr9av/obsidian-wiki3.5k—~2kAutomated safety check: NotesMIT
Obsidian CLIAtmosphere/atmosphere3.8k13 repos~795Automated safety check: PassApache-2.0
Second BrainNicholasSpisak/second-brain7361 repos~1.5kAutomated safety check: NotesNone
LLM Wikilewislulu/llm-wiki-skill655—~3.7kAutomated safety check: PassNone
Obsidian Canvas BoardsAgriciDaniel/claude-obsidian15k—~1.4kAutomated safety check: PassMIT
Youtubeaxoviq-ai/synthadoc1.6k1 repos~634Automated safety check: PassAGPL-3.0-or-later

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Works with

Questions about Graph Colorize

What does Graph Colorize do?

Configure Obsidian graph colors by tag, folder, category, or visibility by updating .obsidian/graph.json. Graph Colorize is an agent skill from Ar9av/obsidian-wiki.json.

When should I use Graph Colorize?

Graph Colorize fits situations like: graph colorization; preserve other graph settings and back up before changes.

How do I install Graph Colorize in Claude Code?

Run `npx skills add Ar9av/obsidian-wiki --skill graph-colorize -a claude-code`. Or copy the skill folder (.skills/graph-colorize in Ar9av/obsidian-wiki) into .claude/skills/graph-colorize in your project. Claude Code loads it when a task matches its description.

How do I install Graph Colorize in Codex?

Run `npx skills add Ar9av/obsidian-wiki --skill graph-colorize -a codex`. Or copy the skill folder (.skills/graph-colorize in Ar9av/obsidian-wiki) into .agents/skills/graph-colorize in your project. Codex loads it when a task matches its description.

Can I use Graph Colorize in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add Ar9av/obsidian-wiki --skill graph-colorize -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/graph-colorize, .gemini/skills/graph-colorize, .github/skills/graph-colorize and .opencode/skills/graph-colorize in your project.

What does Graph Colorize need to run?

SKILL.md names no scripts, command-line tools or credentials: Graph Colorize is instructions for the agent only.

Does Graph Colorize access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Graph Colorize safe to install?

Our automated static check of SKILL.md found notes only (mentions a .env file), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Graph Colorize use?

Graph Colorize is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Graph Colorize use?

About 2k tokens (SKILL.md is roughly 8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Graph Colorize?

Skills that share tags, products or a category with Graph Colorize: Obsidian CLI (Atmosphere/atmosphere, 3.8k stars), Second Brain (NicholasSpisak/second-brain, 736 stars), LLM Wiki (lewislulu/llm-wiki-skill, 655 stars) and Obsidian Canvas Boards (AgriciDaniel/claude-obsidian, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Graph Colorize?

Ar9av (a GitHub user) maintains it in Ar9av/obsidian-wiki, which has 3,532 GitHub stars. The repository holds 39 skills in this directory. The repository was last updated on October 7, 2026.

Source: Ar9av/obsidian-wiki on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.