cobra.summary.summary
¶
Provide the abstract base summary class.
Module Contents¶
Classes¶
Define the abstract base summary. |
Attributes¶
- class cobra.summary.summary.Summary(**kwargs)[source]¶
Bases:
abc.ABC
Define the abstract base summary.
See also
MetaboliteSummary
,ReactionSummary
,ModelSummary
- _generate(model: cobra.Model, solution: Optional[cobra.Solution], fva: Optional[Union[float, pandas.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.
- abstract to_string(names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G', column_width: int = 79) str [source]¶
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(names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G') str [source]¶
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