Visualization

stochastix.utils.visualization.plot_abundance_dynamic

plot_abundance_dynamic(
    ssa_results: SimulationResults,
    species: str | list[str] | tuple[str, ...] = '*',
    time_unit: Literal['s', 'm', 'h', 'd'] = 's',
    figsize: tuple[float, float] = (9, 6),
    line_alpha: float = 0.5,
    log_x_scale: bool = False,
    log_y_scale: bool = False,
    grid_params: dict[str, Any] | None = None,
    ax: Axes | None = None,
    species_labels: list[str] | None = None,
    legend: bool = True,
    base_time_unit: Literal['s', 'm', 'h', 'd'] = 's',
) -> tuple[plt.Figure | None, plt.Axes]

Plot the time evolution of molecular abundances.

Parameters:

• ssa_results (SimulationResults) –

  A SimulationResults object containing time points and abundances.

• species (str | list[str] | tuple[str, ...], default: '*' ) –

  The species to plot. Can be "*" for all species, a single species name, or a list/tuple of species names.

• time_unit (Literal['s', 'm', 'h', 'd'], default: 's' ) –

  The time unit for the x-axis ('s', 'm', 'h', 'd').

• figsize (tuple[float, float], default: (9, 6) ) –

  The figure size (width, height).

• line_alpha (float, default: 0.5 ) –

  The transparency of the plot lines.

• log_x_scale (bool, default: False ) –

  Whether to use a logarithmic scale for the x-axis.

• log_y_scale (bool, default: False ) –

  Whether to use a logarithmic scale for the y-axis.

• grid_params (dict[str, Any] | None, default: None ) –

  A dictionary of parameters for grid customization.

• ax (Axes | None, default: None ) –

  A matplotlib.axes.Axes object to plot on. If None, a new figure and axes are created.

• species_labels (list[str] | None, default: None ) –

  A list of custom labels for the species. If None, the species names from ssa_results are used.

• legend (bool, default: True ) –

  Whether to display the legend.

• base_time_unit (Literal['s', 'm', 'h', 'd'], default: 's' ) –

  Time unit of ssa_results.t (used for conversion to time_unit).

Returns:

• Figure | None –

  A tuple (fig, ax), where fig is the matplotlib.figure.Figure

• Axes –

  object (or None if ax was provided) and ax is the

• tuple[Figure | None, Axes] –

  matplotlib.axes.Axes object.

Raises:

• ValueError –

  If ssa_results is missing required attributes, time_unit is invalid, or a species name is not found.