gephi

Gephi Network Analysis Skill

You have access to 73 MCP tools (prefixed mcp__gephi-mcp__) 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.

Standard Workflow

1. Health check — gephi_health_check (stop if Gephi isn't running)
2. Fresh project — call gephi_create_project before importing
3. Import — gephi_import_file or build with gephi_add_nodes/gephi_add_edges
4. Statistics — compute degree, modularity, etc.
5. Style — color by partition, size by ranking
6. Layout — gephi_run_layout with "ForceAtlas 2", then optionally "Noverlap" and "Label Adjust"
7. Preview — gephi_set_preview_settings for export appearance
8. Export — gephi_export_png (use file param), gephi_export_svg, etc.

Tool Quick Reference

Project & Workspace

gephi_create_project, gephi_open_project, gephi_save_project, gephi_get_project_info, gephi_new_workspace, gephi_list_workspaces, gephi_switch_workspace, gephi_delete_workspace

Graph Construction

gephi_add_node/gephi_add_nodes, gephi_add_edge/gephi_add_edges, gephi_remove_node/gephi_bulk_remove_nodes, gephi_remove_edge, gephi_clear_graph, gephi_set_node_label/gephi_set_edge_label, gephi_set_node_position/gephi_batch_set_positions, gephi_set_edge_weight, gephi_query_nodes/gephi_query_edges

Statistics (run before styling)

• gephi_compute_modularity → creates modularity_class
• gephi_compute_degree → creates degree, indegree, outdegree
• gephi_compute_betweenness → creates betweenesscentrality, closeness, eccentricity
• gephi_compute_pagerank → creates pageranks
• gephi_compute_eigenvector → creates eigencentrality
• gephi_compute_connected_components → creates componentnumber
• gephi_compute_clustering_coefficient → creates clustering
• gephi_compute_avg_path_length → avg path length, diameter
• gephi_compute_hits → creates Authority, Hub

Appearance

gephi_color_by_partition, gephi_color_by_ranking, gephi_size_by_ranking, gephi_set_node_color/gephi_set_node_size, gephi_set_edge_color, gephi_edge_thickness_by_weight, gephi_batch_set_node_colors, gephi_reset_appearance

Layout

gephi_run_layout (use "ForceAtlas 2", "Yifan Hu", "Fruchterman Reingold", "Circular", "Random Layout"), gephi_stop_layout, gephi_get_layout_status, gephi_get_available_layouts, gephi_get_layout_properties/gephi_set_layout_properties

Filtering

gephi_filter_by_degree, gephi_filter_by_edge_weight, gephi_remove_isolates, gephi_extract_ego_network, gephi_extract_giant_component, gephi_reset_filters

Preview & Export

gephi_get_preview_settings/gephi_set_preview_settings, gephi_export_png/gephi_export_pdf/gephi_export_svg (use file param), gephi_export_gexf/gephi_export_graphml/gephi_export_csv

Import

gephi_import_file, gephi_import_gexf/gephi_import_graphml/gephi_import_csv

Styling Defaults

Pastel Community Colors

Always override default Gephi colors with this palette for gephi_color_by_partition:

{"0": [212,222,99], "1": [227,185,216], "2": [89,238,200], "3": [154,226,255], "4": [255,171,125], "5": [255,173,203], "6": [255,220,130], "7": [190,170,230]}

Publication Export Settings

Clean (no labels):

{"node.label.show": false, "edge.opacity": 25, "edge.curved": true, "edge.color": "source", "edge.thickness": 2.0, "node.opacity": 100, "node.border.width": 0.3, "arrow.size": 0}

Labeled:

{"node.label.show": true, "node.label.proportinalSize": false, "node.label.font": "Arial 10 Plain", "node.label.outline.size": 4, "node.label.outline.opacity": 95, "edge.opacity": 15}

Layout

• ForceAtlas 2 for most graphs: {"scalingRatio": 200, "linLogMode": true, "gravity": 1.0, "barnesHutOptimize": true}, 1000-1500 iterations
• Follow with Noverlap (500 iterations, margin 5.0) to push overlapping nodes apart
• Follow with Label Adjust (500 iterations) if labels are enabled

Key Gotchas

• Filters are destructive — they permanently remove nodes/edges. Save project first.
• High gravity (>3) compresses nodes into a ball. Fix: run Random Layout (1 iteration), then re-run ForceAtlas 2.
• Workspace switching can deadlock — if API hangs after workspace switch, Gephi needs restart.
• Press Ctrl+Shift+H in Gephi to center the view on the graph after API operations — the API modifies data but doesn't move the viewport camera.

For detailed tool parameters, see references/tool-reference.md. For layout algorithm details, see references/layout-guide.md. For statistics interpretation, see references/statistics-guide.md.