specimen.classes package

specimen.classes.reports submodule

Classes to generate, handle, manipulate and save reports.

class specimen.classes.reports.SpecimenModelInfoReport(*args: Any, **kwargs: Any)

Bases: ModelInfoReport

A SPECIMEN-specific version of the ModelInfoReport for a given model. Since this report is a child class of the ModelInfoReport of refineGEMs, it inherits its parameters. Attributes below are the newly addes ones.

Attributes:

reac:_origin_counts (dict):

Dictionary with the label of th origin of the reactions as key and the corresponding counts as values.

__annotations__ = {}

__init__(model: cobra.Model) → None

__module__ = 'specimen.classes.reports'

__orig_bases__ = (refinegems.classes.reports.ModelInfoReport,)

format_table() → pandas.DataFrame

Extent the functin format_table to include the reaction origin as set by SPECIMEN.

Returns:

pd.DataFrame:

The information in table format.

save(dir: str, color_palette: str = 'YlGn') → None

Save the report and the

Args:

• dir (str):

  Path to a directory to save the output files to.

• color_palette (str, optional):

  Name of a matplotlib colour palette. Used as the input for the figures. Defaults to ‘YlGn’.

visualise(color_palette: str = 'YlGn') → tuple[matplotlib.figure.Figure]

Extend the visualisation function to include a graph for the creation type.

Args:

• color_palette (str, optional):

  Color palette to be used. Defaults to ‘YlGn’.

Returns:

tuple:

Two graphics (1) and (2):

1. matplotlib.figure.Figure: The original report figure.

2. matplotlib.figure.Figure: Report for the creation origin.