Gephi (GEXF)

Gephi (GEXF)#

GEXF (Graph Exchange XML Format) is commonly used by Gephi and other tools for graph interchange. Graphistry supports GEXF 1.1draft, 1.2draft, and 1.3 for import/export with no extra dependencies.

Use graphistry.gexf() (or graphistry.PlotterBase.PlotterBase.from_gexf()) to load a GEXF file, URL, or stream into a PyGraphistry plotter. By default, any available GEXF viz fields are bound; if the file has no viz data, Graphistry defaults apply.

When to use

  • You have a Gephi (or other tool) export and want to preserve its layout/viz.

  • You need a lightweight interchange format for graph attributes or layouts.

Example

import graphistry

# Preserve GEXF's layout, size, colors, shape icons
g = graphistry.gexf("my_graph.gexf")
g.plot()

# Keep layout while dropping GEXF colors/sizes
g_layout_only = graphistry.gexf(
    "my_graph.gexf",
    bind_node_viz=["position"],
    bind_edge_viz=[],
)
g_layout_only.plot()

For notebook walkthroughs (small + medium GEXF) and dataset samples, see Plugins - Compute & Layout.

Export

You can export a graph to GEXF using graphistry.to_gexf() or graphistry.PlotterBase.PlotterBase.to_gexf():

xml_str = g.to_gexf()
g.to_gexf("out.gexf")

Viz attribute mapping

The loader maps standard GEXF viz attributes into Graphistry bindings:

  • label (node) → point_title

  • label (edge) → edge_title

  • viz:color → point_color / edge_color (hex color strings)

  • viz:size → point_size

  • viz:position → point_x / point_y (and auto-sets play=0)

  • viz:thickness → edge_size

  • viz:color alpha → point_opacity / edge_opacity

  • viz:shape (nodes) → point_icon (FA4 icon names without the fa- prefix: disc→circle, square→square, triangle→caret-up, diamond→diamond; image uses the uri when available)

  • edge weight → edge_weight

Viz binding controls

Use bind_node_viz / bind_edge_viz as allowlists to restrict which GEXF viz fields are bound to Graphistry encodings (unlisted fields still load as columns):

  • node fields: color, size, opacity, position, icon

  • edge fields: color, size, opacity

None (default) binds all supported fields present in the file. Passing an empty list disables all viz bindings for that element type. position binds point_x/point_y and sets play=0 to respect precomputed layouts.

Examples

# Bind all available GEXF viz fields (default)
g = graphistry.gexf("my_graph.gexf")

# Bind no GEXF viz fields (use Graphistry defaults)
g = graphistry.gexf("my_graph.gexf", bind_node_viz=[], bind_edge_viz=[])

# Bind only layout positions for nodes, drop edge viz
g = graphistry.gexf("my_graph.gexf", bind_node_viz=["position"], bind_edge_viz=[])

After loading, you can apply Graphistry’s declarative encodings (for example, encode_point_color or encode_point_size) to override GEXF defaults.

Validation

The loader raises ValueError for common errors such as missing nodes, missing node IDs, or edges that reference unknown nodes. These checks run inside the GEXF loader (XML well-formedness + basic structural checks), not PyGraphistry’s broader graph validation or full GEXF schema validation. For untrusted inputs, install defusedxml; it will be used automatically for safer XML parsing. Use parse_engine="stdlib" or parse_engine="defused" to override the parser (useful in tests).

GEXF import/export helpers.