Plot Overlap Matrix from MBAR

The function plot_mbar_overlap_matrix() allows the user to plot the overlap matrix from overlap_matrix. The user can pass matplotlib.axes.Axes into the function to have the overlap maxtrix drawn on a specific axes. The user could also specify a list of lambda states to be skipped when labelling the states.

Please check How to plot MBAR overlap matrix for usage.

API Reference

alchemlyb.visualisation.plot_mbar_overlap_matrix(matrix: ndarray, skip_lambda_index: list[int] = [], ax: None | Axes = None) → Axes[source]

Plot the MBAR overlap matrix.

Parameters:

  • matrix (numpy.matrix) – DataFrame of the overlap matrix obtained from overlap_matrix

  • skip_lambda_index (List) – list of lambda indices to be omitted from plotting process. Default: [].

  • ax (matplotlib.axes.Axes) – Matplotlib axes object where the plot will be drawn on. If ax=None, a new axes will be generated.

Returns:

An axes with the overlap matrix drawn.

Return type:

matplotlib.axes.Axes

Note

The code is taken and modified from Alchemical Analysis.

Added in version 0.4.0.