pyemma.plots.plot_implied_timescales

pyemma.plots.plot_implied_timescales(ITS, ax=None, outfile=None, show_mle=True, show_mean=True, xlog=False, ylog=True, confidence=0.95, refs=None, nits=- 1, process=None, units='steps', dt=1.0, **kwargs)

Implied timescale plot

Parameters

  • ITS (implied timescales object.) – Object whose data will be plotted. Must provide the functions: get_timescales() and get_timescales(i) where i is the the property samples_available

  • ax (matplotlib Axes object, optional, default = None) – the axes to plot to. When set to None the default Axes object will be used.

  • outfile (str, optional, default = None) – output file to write the figure to. When not given, the plot will be displayed

  • show_mean (bool, default = True) – Line for mean value will be shown, if available

  • show_mle (bool, default = True) – Line for maximum likelihood estimate will be shown

  • xlog (bool, optional, default = False) – Iff true, the x-Axis is logarithmized

  • ylog (bool, optional, default = True) – Iff true, the y-Axis is logarithmized

  • confidence (float, optional, default = 0.95) – The confidence interval for plotting error bars (if available)

  • refs (ndarray((m), dtype=float), optional, default = None) – Reference (exact solution or other reference) timescales if known. The number of timescales must match those in the ITS object

  • nits (integer, default = -1) – Number of implied timescales to be shown. The default behaviour (-1) is to show all timescales available. nits != -1 and process != None are mutually exclusive

  • process (iterable of integers, default is None) – list or ndarray((m), dtype=int) containing a list of the processes to be shown. The default behaviour is to show all timescales available. process != None and nits != -1 are mutually exclusive

  • units (str or list (len=2) of strings, optional, default = 'steps') – Affects the labeling of the axes. Used with dt, allows for changing the physical units of the axes. Accepts simple LaTeX math strings, eg. ‘$mu$s’ If this parameter is a list, it will be assumed that units[0] is for the x-axis and units[1] for the y-axis.

  • dt (float or list(len=2) of floats, optional, default = 1.0) – Physical time between frames, expressed the units given in units. E.g, if you know that each frame corresponds to .010 ns, you can use the combination of parameters dt =0.01, units =’ns’ to display the implied timescales in ns (instead of frames) If this parameter is a list, it will be assumed that dt[0] is for the x-axis and dt[1] for the y-axis.

  • **kwargs (Will be passed to pyplot.plot when plotting the MLE datapoints (not the bootstrapped means)) – See the doc of pyplot for more options. Most useful lineproperties like marker=’o’ and/or :markersize=5

Returns

ax

Return type

Axes object containing the plot