2.1. wc_analysis package

2.1.2. Submodules

2.1.3. wc_analysis._version module

2.1.4. wc_analysis.core module

Analyze knowledge base, model, and simulation results.

Author

Jonathan Karr <karr@mssm.edu>

Date

2018-02-13

Copyright

2018, Karr Lab

License

MIT

class wc_analysis.core.Analysis(out_path=None, options=None)[source]

Bases: object

An analysis of a knowledge base, model, or simulation results

out_path[source]

optional path to save analysis

Type

str

options[source]

options

Type

dict

clean_and_validate_options()[source]

Apply default options and validate options

create_fig(rows=1, cols=1)[source]

Create a figure composed of a grid of subfigures

Parameters

  • rows (int, optional) – number of rows of subfigures

  • cols (int, optional) – number of columns of subfigures

Returns

figure matplotlib.axes.Axes: axes

Return type

matplotlib.figure.Figure

abstract run()[source]

Run the analysis

show_or_save_fig(fig, filename=None)[source]

Show or save a figure

Parameters

  • fig (matplotlib.figure.Figure) – figure

  • filename (str, optional) – filename to save figure

class wc_analysis.core.AnalysisRunner(knowledge_base=None, model=None, sim_results_path=None, analyses=None, out_path=None, options=None)[source]

Bases: object

Run one or more analyses of a whole-cell knowledge base, model, and/or simulation results

knowledge_base[source]

knowledge base

Type

wc_kb.core.KnowledgeBase

model[source]

model

Type

wc_lang.core.Model

sim_results_path[source]

path to simulation results

Type

str

analyses[source]

analyses to run

Type

list of Analysis

out_path[source]

path to save analyses

Type

str

options[source]

options

Type

dict

DEFAULT_ANALYSES = ()[source]
clean_and_validate_options()[source]

Apply default options and validate options

run()[source]

Run multiple analyses

Raises

ValueError – if the analysis is not supported

class wc_analysis.core.KnowledgeBaseAnalysis(knowledge_base, out_path=None, options=None)[source]

Bases: wc_analysis.core.Analysis

Analysis of a knowledge base

knowledge_base[source]

knowledge base

Type

wc_kb.core.KnowledgeBase

class wc_analysis.core.ModelAnalysis(model, knowledge_base=None, out_path=None, options=None)[source]

Bases: wc_analysis.core.Analysis

Analysis of a model

model[source]

model

Type

wc_lang.core.Model

knowledge_base[source]

knowledge base

Type

wc_kb.core.KnowledgeBase

class wc_analysis.core.SimulationAnalysis(sim_results_path, model=None, knowledge_base=None, out_path=None, options=None)[source]

Bases: wc_analysis.core.Analysis

Analysis of a simulation result

sim_results_path[source]

path to simulation results

Type

str

model[source]

model

Type

wc_lang.core.Model

knowledge_base[source]

knowledge base

Type

wc_kb.core.KnowledgeBase

2.1.5. Module contents