Drug-response data analysis (pasmopy.validation)

class pasmopy.validation.CancerCellLineEncyclopedia

Cancer Cell Line Encyclopedia (CCLE) https://portals.broadinstitute.org/ccle

drug_alias

Other drug names.

Type:

dict

_drug_response_data

Pharmacologic profiles for 24 anticancer drugs across 504 cell lines.

Type:

pandas.DataFrame

save_activity_area(expression_ratio, classifier, drug, *, labels, config=None)

Save ActArea.

Return type:

None

Examples

>>> from pasmopy.validation import CancerCellLineEncyclopedia
>>> ErbB_expression_ratio = pd.read_csv(
...     "https://raw.githubusercontent.com/pasmopy/breast_cancer/master/drug_response/data/ErbB_expression_ratio.csv",
...     index_col=0,
... )
>>> ccle = CancerCellLineEncyclopedia()
>>> for drug in ["Erlotinib", "Lapatinib"]:
...     ccle.save_activity_area(
...         ErbB_expression_ratio,
...         {"value": ["high", "low"]},
...         drug,
...         labels=["EGFR high", "EGFR low"],
...     )

save_dose_response_curve(expression_ratio, classifier, drug, *, labels, config=None, show_individual=False)

Save dose-response curves.

Return type:

None

Examples

>>> from pasmopy.validation import CancerCellLineEncyclopedia
>>> ErbB_expression_ratio = pd.read_csv(
...     "https://raw.githubusercontent.com/pasmopy/breast_cancer/master/drug_response/data/ErbB_expression_ratio.csv",
...     index_col=0,
... )
>>> ccle = CancerCellLineEncyclopedia()
>>> for drug in ["Erlotinib", "Lapatinib"]:
...     ccle.save_dose_response_curve(
...         ErbB_expression_ratio,
...         {"value": ["high", "low"]},
...         drug,
...         labels=["EGFR high", "EGFR low"],
...     )