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, skip_lambda_index=[], ax=None)¶ 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
Notes
The code is taken and modified from : Alchemical Analysis