msmexplorer.plot_tpaths¶

msmexplorer.plot_tpaths(msm, sources, sinks, for_committors=None, num_paths=1, pos=None, node_size=None, node_color='pomegranate', edge_color='carbon', alpha=0.7, with_labels=True, ax=None, **kwargs)¶

Plot TPT network diagram.

Parameters:

msm : msmbuilder.msm MSMBuilder MarkovStateModel sources : int or list, optional TPT source states sinks : int or list, optional TPT sink states sinks : ndarray, optional Pre-computed forward committors pos : dict, optional Node positions in dict format (e.g. {node_id : [x, y]}) node_color : str or [r, g, b], optional networkx node colors node_size : int or list, optional networkx node size node_color : str, optional networkx edge color alpha : float, optional (default: 0.7) Opacity of nodes ax : matplotlib axis, optional (default: None) Axis to plot on, otherwise uses current axis. with_labels : boolean, optional Whether or not to include node labels (default: True) **kwargs : dict, optional Extra arguments to pass to networkx.draw_networkx

Returns:

ax : Axis matplotlib figure axis