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 |