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 andprocess
!= 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 andnits
!= -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 parametersdt
=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 parsed to pyplot.plo 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