17.1.1.7.1.3. cobra.summary.reaction_summary
¶
Provide the reaction summary class.
17.1.1.7.1.3.1. Module Contents¶
17.1.1.7.1.3.1.1. Classes¶
Define the reaction summary. |
-
class
cobra.summary.reaction_summary.
ReactionSummary
(*, reaction: Reaction, model: Model, solution: Optional['Solution'] = None, fva: Optional[Union[float, pd.DataFrame]] = None, **kwargs)[source]¶ Bases:
cobra.summary.Summary
Define the reaction summary.
See also
Summary
Parent that defines further attributes.
MetaboliteSummary
,ModelSummary
-
_generate
(self, model: Model, solution: Optional['Solution'], fva: Optional[Union[float, pd.DataFrame]]) → None[source]¶ 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.
-
_string_flux
(self, threshold: float, float_format: str) → str[source]¶ Transform a flux data frame to a string.
-
to_string
(self, names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G', column_width: int = 79) → str[source]¶ Return a pretty string representation of the reaction 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[source]¶ Return a rich HTML representation of the reaction 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