Plotting package

The plots package provides tools to plot scientific data generated by pyEMMA

plots - Plotting tools (pyemma.plots)

User-API

Graph plots

plot_implied_timescales(ITS[, ax, outfile, …])	Implied timescale plot
plot_cktest(cktest[, figsize, diag, y01, …])	Plot of Chapman-Kolmogorov test

Contour plots

plot_density(xall, yall[, ax, cmap, …])	Plot a two-dimensional density map using a histogram of scattered data.
plot_free_energy(xall, yall[, weights, ax, …])	Plot a two-dimensional free energy map using a histogram of scattered data.
plot_contour(xall, yall, zall[, ax, cmap, …])	Plot a two-dimensional contour map by interpolating scattered data on a grid.
plot_state_map(xall, yall, states[, ax, …])	Plot a two-dimensional contour map of states by interpolating labels of scattered data on a grid.
scatter_contour(x, y, z[, ncontours, …])	Contour plot on scattered data (x,y,z) and plots the positions of the points (x,y) on top.

Network plots

plot_markov_model(P[, pos, state_sizes, …])	Network representation of MSM transition matrix
plot_flux(flux[, pos, state_sizes, …])	Network representation of reactive flux
plot_network(weights[, pos, xpos, ypos, …])	Network representation of given matrix

Classes

NetworkPlot(A[, pos, xpos, ypos, ax])

Plot of network with nodes and arcs