17.1.1.7.1.1. cobra.summary.metabolite_summary
¶
Provide the metabolite summary class.
17.1.1.7.1.1.1. Module Contents¶
17.1.1.7.1.1.1.1. Classes¶
Define the metabolite summary. |
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class
cobra.summary.metabolite_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
See also
Summary
Parent that defines further attributes.
ReactionSummary
,ModelSummary
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_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.
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_display_flux
(self, frame: pd.DataFrame, names: bool, threshold: float) → pd.DataFrame[source]¶ 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[source]¶ Create a pretty string representation of the data frame.
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static
_html_table
(frame: pd.DataFrame, float_format: str) → str[source]¶ 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[source]¶ 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
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to_html
(self, 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
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