plot_trans_per_state_vs_time

Plot the number of transitions leading into or out of a given state for each frame in a discrete trajectory as function of time.

Options

-f: Trajectory file. File containing the discrete trajectory stored as numpy.ndarray in the binary .npy format. The array must be of shape (n, f), where n is the number of compounds and f is the number of frames. The shape can also be (f,), in which case the array is expanded to shape (1, f). All elements of the array must be integers or floats whose fractional part is zero, because they are interpreted as the indices of the states in which a given compound is at a given frame.
-o: Output filename.
-b: First frame to read from the trajectory. Frame numbering starts at zero. Default: 0.
-e: Last frame to read from the trajectory. This is exclusive, i.e. the last frame read is actually END - 1. A value of -1 means to read the very last frame. Default: -1.
--every: Read every n-th frame from the trajectory. Default: 1.
--cumsum: Calculate and plot the cumulative sum of transitions per state over time.
--fit: Fit the number of transitions leading into or out of the central state by a power law.
--labels: One label for each state in the discrete trajectory. The labels will be shown in the legend of the plot. If provided, you must give one label for each state. By default the states are numbered consecutively from MIN_STATE to MAX_STATE. Default: None.
--xlim: Left and right limit of the x-axis in data coordinates. Pass ‘None’ to adjust the limit(s) automatically. Default: [None, None].
--ylim: Lower and upper limit of the y-axis in data coordinates. Pass ‘None’ to adjust the limit(s) automatically. Default: [None, None].
--log: Whether to use a logarithmic scale for the x- and/or y-axis. Default: [False, False].