API reference

Cluster plots

plot_voronoi(kmeans[, ax, obs, …]) Plot voronoi regions in a 2D diagram.

MSM plots

plot_pop_resids(msm, **kwargs) Plot residuals between MSM populations and raw counts.
plot_msm_network(msm[, pos, node_size, …]) Plot MSM network diagram.
plot_timescales(msm[, n_timescales, error, …]) Plot MSM timescales spectral diagram.

Projection plots

plot_free_energy(data[, ax, obs, …]) Plot free energy of observable(s) in kilocalories per mole.
plot_histogram(xs[, bins, range, weights, …]) Make a sick corner plot showing the projections of a data set in a multi-dimensional space.

TPT plots

plot_tpaths(msm, sources, sinks[, …]) Plot TPT network diagram.

Miscellaneous plots

plot_chord(data[, ax, cmap, labels, …]) Plot chord diagram from an adjacency matrix.
plot_stackdist(data[, size, aspect, …]) Plot stacked distributions (a.k.a Joy plot) of data.
plot_trace(data[, label, window, ax, …]) Plot trace of time-series data.

Utilities

utils.extract_palette(color_palette) Extract color palette information and return a str/list of hex colors.
utils.make_colormap(color_palette[, N, gamma]) Create a linear colormap from a color palette.
utils.msme_colors(func) A decorator function for enabling MSMExplorer colors.