network_graph

plot.network_graph

Network graph plotting utilities.

Three rendering backends:

1. networkx — standard nx.draw_networkx_* rendering
2. bsplot — text-box nodes + curved edges via bsplot.graph
3. brain — 3-D brain surface with sphere nodes + tube edges via bsplot.graph.plot_network_on_surface

Functions

Name	Description
plot_graph_brain	Render a network on the cortical brain surface using bsplot.
plot_graph_bsplot	Render a network graph with bsplot text-box nodes and curved edges.
plot_graph_networkx	Render a network graph with standard NetworkX drawing.

plot_graph_brain

plot.network_graph.plot_graph_brain(
    network,
    *,
    ax=None,
    template='fsaverage',
    density='164k',
    hemi=('lh', 'rh'),
    view='lateral',
    surface_alpha=0.3,
    threshold_percentile=90,
    node_radius=1.5,
    node_color='auto',
    node_cmap='YlOrRd',
    node_data_key='strength',
    node_scale=None,
    edge_radius=0.15,
    edge_color='steelblue',
    edge_cmap=None,
    edge_data_key='weight',
    edge_scale=None,
    annot_dir='/Applications/freesurfer/7.4.1/subjects/fsaverage/label',
    figsize=(6, 5),
    **kwargs,
)

Render a network on the cortical brain surface using bsplot.

Nodes are rendered as coloured spheres at parcel centroids; edges as coloured tubes between them. Only cortical parcels that can be matched to the FreeSurfer aparc annotation are shown.

Parameters

network : Network Network object with a parcellation atlas. ax : Axes, optional If None, a new figure is created. template : str Surface template ("fsaverage"). density : str Surface mesh density ("164k"). hemi : str or tuple "lh", "rh", or ("lh", "rh"). view : str Camera view ("lateral", "top", "front", etc.). surface_alpha : float Brain surface transparency. threshold_percentile : float Only render edges above this percentile weight. node_radius : float Sphere radius for nodes. node_color : str Uniform colour (or "auto" to use node_cmap). node_cmap : str Colormap for node data. node_data_key : str Node attribute for colour mapping (default "strength"). node_scale : dict, optional Radius scaling, e.g. {"strength": 2, "mode": "exp"}. edge_radius : float Tube radius for edges. edge_color : str Uniform edge colour (used when edge_cmap is None). edge_cmap : str, optional Colormap for edge data. edge_data_key : str Edge attribute for colour mapping. edge_scale : dict, optional Tube radius scaling, e.g. {"weight": 8, "mode": "exp"}. annot_dir : str Path to FreeSurfer fsaverage/label/ directory. figsize : tuple Figure size if no ax is given. **kwargs Forwarded to bsplot.graph.plot_network_on_surface.

Returns

fig : Figure ax : Axes mappables : dict ScalarMappable objects (keys "nodes" / "edges").

plot_graph_bsplot

plot.network_graph.plot_graph_bsplot(
    G,
    *,
    ax=None,
    node_cmap='viridis',
    edge_cmap='viridis',
    node_color_by='in-strength',
    log_in_strength=True,
    edge_color_by='type',
    pos=None,
    node_labels=True,
    edge_labels=True,
    fontsize=8,
    edge_radius=0.1,
    linewidth=1.5,
    alpha=0.9,
)

Render a network graph with bsplot text-box nodes and curved edges.

Requires bsplot to be installed.

Parameters

G : networkx.MultiDiGraph Graph (typically from Network.graph). ax : Axes, optional If None, a new figure is created and returned. node_cmap, edge_cmap : str or Colormap Colormaps for nodes / edges. node_color_by : str "in-strength" or "node". log_in_strength : bool Apply log1p to in-strength. edge_color_by : str Edge attribute used for colour classification (default "type"). pos : dict {node: (x, y)}. If None, spring layout is used. node_labels, edge_labels : bool Toggle label rendering. fontsize : float Label font size. edge_radius : float Curvature radius for edges. linewidth : float Edge line width. alpha : float Node box transparency.

Returns

Figure (when ax is None) or ScalarMappable (when ax given).

plot_graph_networkx

plot.network_graph.plot_graph_networkx(
    G,
    *,
    ax=None,
    node_cmap='viridis',
    edge_cmap='viridis',
    node_color_by='in-strength',
    node_size_by='in-strength',
    node_size_scaling=100,
    log_in_strength=True,
    edge_color_by='weight',
    pos=None,
    node_labels=True,
    edge_labels=True,
    fontsize=8,
    edge_kwargs=None,
    node_kwargs=None,
)

Render a network graph with standard NetworkX drawing.

Parameters

G : networkx.MultiDiGraph Graph (typically from Network.graph). ax : Axes, optional If None, a new figure is created and returned. node_cmap, edge_cmap : str or Colormap Colormaps for nodes / edges. node_color_by : str "in-strength" or "node" (index-based). node_size_by : str or float "in-strength" for proportional sizing, or a fixed float. node_size_scaling : float Scaling factor for node circles. log_in_strength : bool Apply log1p to node in-strength. edge_color_by : str Edge attribute used for colour mapping. pos : dict {node: (x, y)}. If None, spring layout is used. node_labels, edge_labels : bool Toggle label rendering. fontsize : float Label font size. edge_kwargs, node_kwargs : dict Extra kwargs forwarded to nx.draw_networkx_edges / nx.draw_networkx_nodes.

Returns

Figure (when ax is None) or ScalarMappable (when ax given).