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_free_energy(xall, yall[, weights, ax, ...]) Free energy plot given 2D scattered data
scatter_contour(x, y, z[, ncontours, ...]) Contour plot on scattered data (x,y,z) and the 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