viz#

Network visualization and plotting (viz).

The visualization module provides a flexible plotting system for phylogenetic networks and graphs with support for multiple layout algorithms and customizable styling. Use plot() for all supported types. It dispatches by object type:

Plotting#

phylozoo.viz.plot(obj: Any, layout: str = 'auto', style: Any = None, ax: Any | None = None, show: bool = False, **kwargs: Any) → Any[source]#

Plot a phylogenetic network or graph.

Dispatches by object type: DirectedPhyNetwork, SemiDirectedPhyNetwork, DirectedMultiGraph, or MixedMultiGraph. Use layout=’auto’ for the default layout per type, or specify a layout name.

Parameters:

  • obj (DirectedPhyNetwork | SemiDirectedPhyNetwork | DirectedMultiGraph | MixedMultiGraph) – The network or graph to plot.

  • layout (str, optional) – Layout algorithm. Use ‘auto’ for the default per type. DirectedPhyNetwork: ‘pz-dag’ (default), or NetworkX (‘spring’, ‘circular’, ‘kamada_kawai’, ‘planar’, ‘random’, ‘shell’, ‘spectral’, ‘spiral’, ‘bipartite’) or Graphviz (‘dot’, ‘neato’, ‘fdp’, ‘sfdp’, ‘twopi’, ‘circo’). SemiDirectedPhyNetwork: ‘twopi’ (default), ‘pz-radial’ (trees only), or NetworkX/Graphviz. DirectedMultiGraph / MixedMultiGraph: NetworkX or Graphviz only (no PhyloZoo layouts). By default ‘auto’.

  • style (DNetStyle | SDNetStyle | DMGraphStyle | MGraphStyle, optional) – Styling configuration. If None, uses default style for the object type. By default None.

  • ax (matplotlib.axes.Axes, optional) – Existing axes to plot on. If None, creates new figure and axes. By default None.

  • show (bool, optional) – If True, automatically display the plot using plt.show(). By default False.

  • **kwargs – Additional parameters for layout computation (e.g. layer_gap, leaf_gap for pz-dag).

Returns:

The axes object containing the plot.

Return type:

matplotlib.axes.Axes

Raises:

Examples

>>> from phylozoo import DirectedPhyNetwork
>>> from phylozoo.viz import plot
>>>
>>> net = DirectedPhyNetwork(
...     edges=[(3, 1), (3, 2)],
...     nodes=[(1, {'label': 'A'}), (2, {'label': 'B'})]
... )
>>> ax = plot(net)
>>> ax = plot(net, layout='spring', show=True)

Submodules#