petab.visualize.plotter
PEtab visualization plotter classes
Classes
|
Matplotlib wrapper |
|
Plotter abstract base class. |
|
Seaborn wrapper. |
- class petab.visualize.plotter.MPLPlotter(figure: Figure, data_provider: DataProvider)[source]
Bases:
Plotter
Matplotlib wrapper
- static _error_column_for_plot_type_data(plot_type_data: str) Optional[str] [source]
Translate PEtab plotTypeData value to column name of internal data representation
- Parameters:
plot_type_data (PEtab plotTypeData value (the way replicates) –
handled) (should be) –
- Return type:
Name of corresponding column
- static _line_plot_at_t_inf(ax: Axes, plotTypeData: str, measurements_to_plot: DataSeries, simulations_to_plot: DataSeries, noise_col: str, label_base: str, split_axes_params: dict, color=None) Tuple[Axes, Axes] [source]
Plot data at t=inf.
- Parameters:
ax – Axis object for the data corresponding to the finite timepoints.
plotTypeData – The way replicates should be handled.
measurements_to_plot – Measurements to plot.
simulations_to_plot – Simulations to plot.
noise_col – The name of the error column for plot_type_data.
label_base – Label base.
split_axes_params – A dictionary of split axes parameters with - Axis object for the data corresponding to t=inf - Time value that represents t=inf - left and right limits for the axis where the data corresponding to the finite timepoints is plotted
color – Line color.
- Returns:
Two axis objects (for the data corresponding to the finite timepoints)
and for the data corresponding to t=inf
- static _postprocess_splitaxes(ax: Axes, ax_inf: Axes, t_inf: float) None [source]
Postprocess the splitaxes: set axes limits, turn off unnecessary ticks and plot dashed lines highlighting the gap in the x axis.
- Parameters:
ax – Axis object for the data corresponding to the finite timepoints.
ax_inf – Axis object for the data corresponding to t=inf.
t_inf – Time value that represents t=inf
- _preprocess_splitaxes(fig: Figure, ax: Axes, subplot: Subplot) Dict [source]
Prepare splitaxes if data at t=inf should be plotted: compute left and right limits for the axis where the data corresponding to the finite timepoints will be plotted, compute time point that will represent t=inf on the plot, create additional axes for plotting data at t=inf.
- static _square_plot_equal_ranges(ax: Axes, lim: Optional[Union[List, Tuple]] = None) Axes [source]
Square plot with equal range for scatter plots.
- Return type:
Updated axis object.
- generate_barplot(ax: Axes, dataplot: DataPlot, plotTypeData: str) None [source]
Generate barplot.
- Parameters:
ax – Axis object.
dataplot – Visualization settings for the plot.
plotTypeData – Specifies how replicates should be handled.
- generate_figure(subplot_dir: Optional[str] = None, format_: str = 'png') Optional[Dict[str, Axes]] [source]
Generate the full figure based on the markup in the figure attribute.
- Parameters:
subplot_dir – A path to the folder where single subplots should be saved. PlotIDs will be taken as file names.
format – File format for the generated figure. (See
matplotlib.pyplot.savefig()
for supported options).
- Returns:
ax – Axis object of the created plot.
None – In case subplots are saved to file.
- generate_lineplot(ax: Axes, dataplot: DataPlot, plotTypeData: str, splitaxes_params: dict) Tuple[Axes, Axes] [source]
Generate lineplot.
It is possible to plot only data or only simulation or both.
- Parameters:
ax – Axis object.
dataplot – Visualization settings for the plot.
plotTypeData – Specifies how replicates should be handled.
splitaxes_params –
- class petab.visualize.plotter.Plotter(figure: Figure, data_provider: DataProvider)[source]
Bases:
ABC
Plotter abstract base class.
- figure
Figure instance that serves as a markup for the figure that should be generated
- data_provider
Data provider
- class petab.visualize.plotter.SeabornPlotter(figure: Figure, data_provider: DataProvider)[source]
Bases:
Plotter
Seaborn wrapper.