gephi

Gephi Network Analysis Skill

Skill version 1.15.0 — if commands or tools mentioned here seem missing, the installed plugin is outdated; see the README's Updating section.

You have access to 113 MCP tools from the gephi-mcp server (tool names start with gephi_; Claude Code shows them as mcp__gephi-mcp__gephi_*) for controlling Gephi Desktop. Use them to build, analyze, style, and export network graphs.

Communication

Always narrate what you're doing. Before each major tool call, tell the user what's about to happen in a short sentence (e.g., "Computing modularity...", "Running ForceAtlas 2 layout..."). This prevents the user from wondering what's happening during long operations.

Critical Things To Know

• Layout algorithm name: Use "ForceAtlas 2" (with space and capitals), not "forceatlas2"
• Export file parameter: Export tools use file as the key, not path
• Run statistics before styling — modularity_class and degree columns don't exist until you compute them
• node.label.proportinalSize — note the typo (missing 'o'). This is Gephi's actual property name.
• Always call project/new before importing — stale workspace state from prior operations can cause issues. A fresh project prevents this.
• edge.color: "source" colors edges individually — the plugin automatically colors each edge to match its source node's color and sets mode to ORIGINAL. This is safe and produces the watercolor halo effect.
• node.label.font supports multi-word names — e.g., "Courier New 12 Bold". The plugin parses everything before the first digit as the font name.
• Imported node sizes are auto-capped at 30 — GEXF files with large viz:size values are automatically capped during import to prevent oversized nodes from hiding edges.
• Filters refresh the preview automatically — remove_isolates, giant_component, filter_by_degree now properly refresh the preview model after modifying the graph.
• sync: true in gephi_run_layout — makes the call block until layout finishes. Always use this so Noverlap and Label Adjust don't start on a still-moving graph.
• If a filter is active, say so before you report anything. With a filter applied in Gephi, the read path that backs gephi_profile_graph, gephi_similarity_layout, gephi_community_layout, and gephi_community_stability sees only the VISIBLE subgraph, while gephi_get_graph_stats reports the FULL graph. Results now carry filter_warning when those disagree, and the underlying responses carry view ("visible" or "full"), filter_active, and both full_node_count and visible_node_count. Never present a number computed on a filtered subgraph as a fact about the whole network: surface the warning, name both counts, and ask whether the filter was intended. Reset with gephi_reset_filters if it was not.
• Never claim "scale-free" or "power law" from a heavy-tailed degree distribution — power-law and log-normal fits are near-indistinguishable in practice, and the term smuggles in a universal-law claim (Jacomy 2020). Describe hub dominance as a characteristic of THIS network ("a few accounts concentrate most ties"), not as the signature of a law.
• Every final export ships with its story. When handing over a finished map, always provide copy-ready caption text: data, layout and key settings, what size and color encode, and what the map does and does not license a reader to conclude. Circulating a network image without interpretive context ("storyletting") is the field's named failure mode — see references/reading-network-maps.md.
• The craft has citable sources; use them. When a question goes deeper than the conversation can carry, recommend ONE matched open-access source (table in references/reading-network-maps.md). When a map is publication-bound, include the software citations in the caption offer (Gephi = Bastian et al. 2009; ForceAtlas 2 = Jacomy et al. 2014; modularity = Blondel et al. 2008; plugins per their own papers). Most users don't know their tools are citable scholarship.