BioSimSpace.Notebook.plotOverlapMatrix¶

BioSimSpace.Notebook.plotOverlapMatrix(overlap, continuous_cbar=False, color_bar_cutoffs=[0.03, 0.1, 0.3])[source]¶

Plot the overlap matrix from a free-energy perturbation analysis.

Parameters:

overlap (List of List of float, or 2D numpy array of float) – The overlap matrix.
continuous_cbar (bool, optional, default=False) – If True, use a continuous colour bar. Otherwise, use a discrete set of values defined by the ‘color_bar_cutoffs’ argument to assign a colour to each element in the matrix.
color_bar_cutoffs (List of float, optional, default=[0.03, 0.1, 0.3]) – The cutoffs to use when assigning a colour to each element in the matrix. This is used for both the continuous and discrete color bars. Can not contain more than 3 elements.