Changelog

v1.2.0 (Development)

New Features

Improvements

API Changes

v1.1.0 (January 5, 2018)

New Features

  • Added a new function plot_angles that plots the distribution of an angle in polar coordinates and a regular distribution plot (#119).
  • Added a new function plot_stackdist that plots stacked distributions (a.k.a joy plots) of data (#102).
  • Added a new function plot_implied_timescales that accepts a list of msm objects calculated at different lag times. Returns an implied timescales plot (#90).
  • plot_free_energy now accepts a return_data flag that will return the data used for the free energy plot(#78).
  • Added a new function plot_trace2d that plots the time evolution of a 2D numpy array using a colorbar to map the time (#108).
  • Added a new function plot_decomp_grid that projects a 1D decomposition

onto a 2D grid (#115).

Improvements

  • vmin in plot_free_energy is now set to 1E-12 unless otherwise specialized.
  • Add plot_implied_timescales example to the Fs-Peptide-Example.ipynb notebook. Also added some minor clarifications and explanations (#107).

v1.0.0 (March 30, 2017)

New Features

  • plot_free_energy now accepts two extra arguments, cbar and cbar_kwargs to add a colorbar and control its aesthetics (#73).

Improvements

  • The shade option now works for plot_free_energy in the 1D case (#76).
  • Fixed an issue where adding cluster centers would break the visualization if ndim > 2 (#70).

v0.3.0 (October 24, 2016)

API Changes

  • side_ax in plot_trace is now optional if ax is provided (#54)
  • legend in plot_trace now defaults to True if label is provided, otherwise false. It previously always defaulted to True (#54).
  • plot_voronoi accepts a new parameter alpha (#55).
  • plot_voronoi will not set axis limits if you specify ax (#55).

Improvements

  • plot_msm_network and plot_tpaths can now handle lists as node_color and node_size (#61).
  • extract_palette can now handle rgb tuples and lists (#61).

v0.2.0 (September 15, 2016)

We’re pleased to announce the release of MSMExplorer v0.2.0. The focus of this release is improving plotting reproducibility and utilities. There is also a major bugfix for plot_chord and plot_free_energy. We encourage all users to update to v0.2.0.

API Changes

  • darkslategrey has been renamed to carbon (#41).
  • plot_free_energy now supports a random_state option (#40)

New Features

  • example_datasets has been added. This allows example datasets to be pulled from the msmb_data package (#41).
  • make_colormap has been added in msmexplorer.utils. It creates a linear colormap from a color palette (#40).
  • msme_colors has been added in msmexplorer.utils. It allows any non-native plotting functions to handle MSMExplorer color strings (#40).

Improvements

  • Test coverage is greatly improved (#43)
  • plot_free_energy now produces correct 1-D free energy plots (#43).
  • extract_palette is now more robust (#40).
  • Improve example reproducibility (#40)
  • Fix path vertices problem in plot_chord (#38).

v0.1.0 (August 30, 2016)

This is the first stable version of MSMExplorer

New Features

  • Clustering plots: plot_voronoi
  • MSM plots: plot_pop_resids, plot_msm_network, plot_timescales
  • Projection plots: plot_free_energy, plot_histogram
  • TPT plots: plot_tpaths
  • Misc. plots: plot_chord, plot_trace