petab.visualize.plotting

PEtab visualization data selection and visualization settings classes

Classes

DataPlot(plot_settings)	Visualization specification of a plot of one data series, e.g. for an individual line on a subplot.
DataProvider(exp_conditions[, ...])	Handles data selection.
DataSeries(conditions_[, data_to_plot])	Data for one individual line
Figure([subplots, size, title])	Visualization specification of a figure.
Subplot(plot_id, plot_settings[, dataplots])	Visualization specification of a subplot.
VisSpecParser(conditions_data[, exp_data, ...])	Parser of visualization specification provided by user either in the form of Visualization table or as a list of lists with datasets ids or observable ids or condition ids.

class petab.visualize.plotting.DataPlot(plot_settings: dict)

Bases: object

Visualization specification of a plot of one data series, e.g. for an individual line on a subplot.

class petab.visualize.plotting.DataProvider(exp_conditions: DataFrame, measurements_data: DataFrame | None = None, simulations_data: DataFrame | None = None)

Bases: object

Handles data selection.

get_data_series(data_df: DataFrame, data_col: Literal['measurement', 'simulation'], dataplot: DataPlot, provided_noise: bool) → DataSeries

Get data to plot from measurement or simulation DataFrame.

Parameters:

• data_df (measurement or simulation DataFrame)

• data_col (data column, i.e. 'measurement' or 'simulation')

• dataplot (visualization specification)

• provided_noise – True if numeric values for the noise level are provided in the data table

Return type:

Data to plot

get_data_to_plot(dataplot: DataPlot, provided_noise: bool) → Tuple[DataSeries, DataSeries]

Get data to plot.

Parameters:

• dataplot (visualization specification)

• provided_noise – True if numeric values for the noise level are provided in the measurement table

Returns:

• measurements_to_plot,

• simulations_to_plot

class petab.visualize.plotting.DataSeries(conditions_: ndarray | Series | None, data_to_plot: DataFrame | None = None)

Bases: object

Data for one individual line

add_offsets(x_offset=0, y_offset=0) → None

Data offsets.

Parameters:

• x_offset – Offset for the independent variable.

• y_offset – Offsets for the observable.

add_x_offset(offset) → None

Offset for the independent variable.

Parameters:

offset – Offset value.

class petab.visualize.plotting.Figure(subplots: List[Subplot] | None = None, size: Tuple = [20, 15], title: Tuple | None = None)

Bases: object

Visualization specification of a figure.

Contains information regarding how data should be visualized.

add_subplot(subplot: Subplot) → None

Add subplot.

Parameters:

subplot – Subplot visualization settings.

save_to_tsv(output_file_path: str = 'visuSpec.tsv') → None

Save full Visualization specification table.

Note that datasetId column in the resulting table might have been generated even though datasetId column in Measurement table is missing or is different. Please, correct it manually.

Parameters:

output_file_path – File path to which the generated visualization specification is saved.

set_axes_limits(xlim: Tuple[Real | None, Real | None] | None = None, ylim: Tuple[Real | None, Real | None] | None = None) → None

Set axes limits for all subplots. If xlim or ylim or any of the tuple items is None, corresponding limit is left unchanged.

Parameters:

• xlim – X axis limits.

• ylim – Y axis limits.

class petab.visualize.plotting.Subplot(plot_id: str, plot_settings: dict, dataplots: List[DataPlot] | None = None)

Bases: object

Visualization specification of a subplot.

add_dataplot(dataplot: DataPlot) → None

Add data plot.

Parameters:

dataplot – Data plot visualization settings.

set_axes_limits(xlim: Tuple[Real | None, Real | None] | None = None, ylim: Tuple[Real | None, Real | None] | None = None)

Set axes limits for all subplots. If xlim or ylim or any of the tuple items is None, corresponding limit is left unchanged.

Parameters:

• xlim – X axis limits.

• ylim – Y axis limits.

class petab.visualize.plotting.VisSpecParser(conditions_data: str | Path | DataFrame, exp_data: str | Path | DataFrame | None = None, sim_data: str | Path | DataFrame | None = None)

Bases: object

Parser of visualization specification provided by user either in the form of Visualization table or as a list of lists with datasets ids or observable ids or condition ids. Figure instance is created containing information regarding how data should be visualized. In addition to the Figure instance, a DataProvider instance is created that will be responsible for the data selection and manipulation.

static create_subplot(plot_id: str, subplot_vis_spec: DataFrame) → Subplot

Create subplot.

Parameters:

• plot_id – Plot id.

• subplot_vis_spec – A visualization specification DataFrame that contains specification for the subplot and corresponding dataplots.

Return type:

Subplot

parse_from_id_list(ids_per_plot: List[List[str]] | None = None, group_by: str = 'observable', plotted_noise: str | None = 'MeanAndSD') → Tuple[Figure, DataProvider]

Get visualization settings from a list of ids and a grouping parameter.

Parameters:

• ids_per_plot –

  A list of lists. Each sublist corresponds to a plot, each subplot contains the Ids of datasets or observables or simulation conditions for this plot. e.g.

  dataset_ids_per_plot = [['dataset_1', 'dataset_2'],
                          ['dataset_1', 'dataset_4',
                           'dataset_5']]
  

  or

  cond_id_list = [['model1_data1'],
                  ['model1_data2', 'model1_data3'],
                  ['model1_data4', 'model1_data5'],
                  ['model1_data6']].
  

• group_by – Grouping type. Possible values: ‘dataset’, ‘observable’, ‘simulation’.

• plotted_noise – String indicating how noise should be visualized: [‘MeanAndSD’ (default), ‘MeanAndSEM’, ‘replicate’, ‘provided’].

Return type:

A figure template with visualization settings and a data provider

parse_from_vis_spec(vis_spec: str | Path | DataFrame | None) → Tuple[Figure, DataProvider]

Get visualization settings from a visualization specification.

Parameters:

vis_spec – Visualization specification DataFrame in the PEtab format or a path to a visualization file.

Return type:

A figure template with visualization settings and a data provider