17.1.1.7. cobra.summary
¶
17.1.1.7.1. Submodules¶
17.1.1.7.2. Package Contents¶
17.1.1.7.2.1. Classes¶
Define the abstract base summary. |
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Define the metabolite summary. |
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Define the model summary. |
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class
cobra.summary.
Summary
(**kwargs)[source]¶ Bases:
abc.ABC
Define the abstract base summary.
See also
MetaboliteSummary
,ReactionSummary
,ModelSummary
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_generate
(self, model: Model, solution: Optional['Solution'], fva: Optional[Union[float, pd.DataFrame]]) → None¶ Prepare the data for the summary instance.
- Parameters
model (cobra.Model) – The metabolic model for which to generate a metabolite summary.
solution (cobra.Solution, optional) – A previous model solution to use for generating the summary. If
None
, the summary method will generate a parsimonious flux distribution.fva (pandas.DataFrame or float, optional) – Whether or not to include flux variability analysis in the output. If given, fva should either be a previous FVA solution matching the model or a float between 0 and 1 representing the fraction of the optimum objective to be searched.
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__str__
(self) → str¶ Return a string representation of the summary.
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_repr_html_
(self) → str¶ Return a rich HTML representation of the summary.
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property
tolerance
(self) → float¶ Return the set threshold.
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_normalize_threshold
(self, threshold: Optional[float])¶ Return a sensible threshold value.
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abstract
to_string
(self, names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G', column_width: int = 79) → str¶ Return a pretty string representation of the summary.
- Parameters
names (bool, optional) – Whether or not elements should be displayed by their common names (default False).
threshold (float, optional) – Hide fluxes below the threshold from being displayed. If no value is given, the model tolerance is used (default None).
float_format (str, optional) – Format string for floats (default ‘.4G’).
column_width (int, optional) – The maximum column width for each row (default 79).
- Returns
The summary formatted as a pretty string.
- Return type
-
abstract
to_html
(self, names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G') → str¶ Return a rich HTML representation of the metabolite summary.
- Parameters
names (bool, optional) – Whether or not elements should be displayed by their common names (default False).
threshold (float, optional) – Hide fluxes below the threshold from being displayed. If no value is given, the model tolerance is used (default None).
float_format (str, optional) – Format string for floats (default ‘.4G’).
- Returns
The summary formatted as HTML.
- Return type
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to_frame
(self) → pd.DataFrame¶ Return the a data frame representation of the summary.
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class
cobra.summary.
MetaboliteSummary
(*, metabolite: Metabolite, model: Model, solution: Optional['Solution'] = None, fva: Optional[Union[float, pd.DataFrame]] = None, **kwargs)[source]¶ Bases:
cobra.summary.Summary
Define the metabolite summary.
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producing_flux
¶ A pandas DataFrame of only the producing fluxes.
- Type
pandas.DataFrame
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consuming_flux
¶ A pandas DataFrame of only the consuming fluxes.
- Type
pandas.DataFrame
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_generate
(self, model: Model, solution: Optional['Solution'], fva: Optional[Union[float, pd.DataFrame]]) → None¶ Prepare the data for the summary instance.
- Parameters
model (cobra.Model) – The metabolic model for which to generate a metabolite summary.
solution (cobra.Solution, optional) – A previous model solution to use for generating the summary. If
None
, the summary method will generate a parsimonious flux distribution.fva (pandas.DataFrame or float, optional) – Whether or not to include flux variability analysis in the output. If given, fva should either be a previous FVA solution matching the model or a float between 0 and 1 representing the fraction of the optimum objective to be searched.
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_display_flux
(self, frame: pd.DataFrame, names: bool, threshold: float) → pd.DataFrame¶ Transform a flux data frame for display.
- Parameters
- Returns
The transformed pandas DataFrame with flux percentages and reaction definitions.
- Return type
pandas.DataFrame
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static
_string_table
(frame: pd.DataFrame, float_format: str, column_width: int) → str¶ Create a pretty string representation of the data frame.
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static
_html_table
(frame: pd.DataFrame, float_format: str) → str¶ Create an HTML representation of the data frame.
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to_string
(self, names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G', column_width: int = 79) → str¶ Return a pretty string representation of the metabolite summary.
- Parameters
names (bool, optional) – Whether or not elements should be displayed by their common names (default False).
threshold (float, optional) – Hide fluxes below the threshold from being displayed. If no value is given, the model tolerance is used (default None).
float_format (str, optional) – Format string for floats (default ‘.4G’).
column_width (int, optional) – The maximum column width for each row (default 79).
- Returns
The summary formatted as a pretty string.
- Return type
-
to_html
(self, names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G') → str¶ Return a rich HTML representation of the metabolite summary.
- Parameters
names (bool, optional) – Whether or not elements should be displayed by their common names (default False).
threshold (float, optional) – Hide fluxes below the threshold from being displayed. If no value is given, the model tolerance is used (default None).
float_format (str, optional) – Format string for floats (default ‘.4G’).
- Returns
The summary formatted as HTML.
- Return type
-
-
class
cobra.summary.
ModelSummary
(*, model: Model, solution: Optional['Solution'] = None, fva: Optional[Union[float, pd.DataFrame]] = None, **kwargs)[source]¶ Bases:
cobra.summary.Summary
Define the model summary.
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uptake_flux
¶ A pandas DataFrame of only the uptake fluxes.
- Type
pandas.DataFrame
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secretion_flux
¶ A pandas DataFrame of only the consuming fluxes.
- Type
pandas.DataFrame
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_generate
(self, model: Model, solution: Optional['Solution'], fva: Optional[Union[float, pd.DataFrame]]) → None¶ Prepare the data for the summary instance.
- Parameters
model (cobra.Model) – The metabolic model for which to generate a metabolite summary.
solution (cobra.Solution, optional) – A previous model solution to use for generating the summary. If
None
, the summary method will generate a parsimonious flux distribution.fva (pandas.DataFrame or float, optional) – Whether or not to include flux variability analysis in the output. If given, fva should either be a previous FVA solution matching the model or a float between 0 and 1 representing the fraction of the optimum objective to be searched.
-
_display_flux
(self, frame: pd.DataFrame, names: bool, element: str, threshold: float) → pd.DataFrame¶ Transform a flux data frame for display.
- Parameters
- Returns
The transformed pandas DataFrame with flux percentages and reaction definitions.
- Return type
pandas.DataFrame
-
static
_string_table
(frame: pd.DataFrame, float_format: str, column_width: int) → str¶ Create a pretty string representation of the data frame.
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static
_html_table
(frame: pd.DataFrame, float_format: str) → str¶ Create an HTML representation of the data frame.
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_string_objective
(self, names: bool) → str¶ Return a string representation of the objective.
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to_string
(self, names: bool = False, element: str = 'C', threshold: Optional[float] = None, float_format: str = '.4G', column_width: int = 79) → str¶ Return a pretty string representation of the model summary.
- Parameters
names (bool, optional) – Whether or not elements should be displayed by their common names (default False).
element (str, optional) – The atomic element to summarize uptake and secretion for (default ‘C’).
threshold (float, optional) – Hide fluxes below the threshold from being displayed. If no value is given, the model tolerance is used (default None).
float_format (str, optional) – Format string for floats (default ‘.4G’).
column_width (int, optional) – The maximum column width for each row (default 79).
- Returns
The summary formatted as a pretty string.
- Return type
-
to_html
(self, names: bool = False, element: str = 'C', threshold: Optional[float] = None, float_format: str = '.4G') → str¶ Return a rich HTML representation of the model summary.
- Parameters
names (bool, optional) – Whether or not elements should be displayed by their common names (default False).
element (str, optional) – The atomic element to summarize uptake and secretion for (default ‘C’).
threshold (float, optional) – Hide fluxes below the threshold from being displayed. If no value is given, the model tolerance is used (default None).
float_format (str, optional) – Format string for floats (default ‘.4G’).
- Returns
The summary formatted as HTML.
- Return type
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