function plot_adjacency

deeptime.plots.plot_adjacency(adjacency_matrix, positions: Optional[ndarray] = None, layout=None, ax=None, scale_states=True)

Plot an adjacency matrix. The edges are scaled according to the respective values. For more fine-grained control use Network.

(Source code, png, hires.png, pdf)

../../_images/deeptime-plots-plot_adjacency-1.png
Parameters:

  • adjacency_matrix (ndarray or scipy sparse matrix) – Adjacency matrix to plot. Could be, e.g., a MSM transition matrix.

  • positions (ndarray, optional, default=None) – A (N, 2)-shaped ndarray containing positions for the nodes of the adjacency matrix. If left as None, the layout is algorithmically determined (based on the algorithm specified in the layout parameter).

  • layout (callable, optional, default=None) – The automatic layout to use. Only has an effect, if positions is None. In that case, it defaults to the networkx.spring_layout. Can be any callable which takes a networkx graph as first argument and yields a position array or dict.

  • ax (matplotlib.axes.Axes, optional, default=None) – The axes to plot on. Otherwise, uses the current axes (via plt.gca()).

  • scale_states (bool, default=True) – Whether to scale nodes according to the value on the diagonal of the adjacency matrix.

Returns:

ax – The axes that were plotted on.

Return type:

matplotlib.axes.Axes

See also

Network