Cancer Types

The module cancer_types provides functions related to Cancer Types section of cBioPortal Web Public API.

pybioportal.cancer_types.get_all_cancer_types(direction='ASC', pageNumber=0, pageSize=10000000, projection='SUMMARY', sortBy=None)

Get all cancer types from cBioPortal.

Parameters:

• direction (str) –

  Direction of the sort.

  Possible values:

  • ”ASC”: Ascending (default).

  • ”DESC”: Descending.

• pageNumber (int) –

  Page number of the result list.

  • Minimum value is 0.

• pageSize (int) –

  Page size of the result list.

  • Minimum value is 1, maximum value is 10000000.

• projection (str) –

  Level of detail of the response.

  Possible values:

  • ”DETAILED”: Detailed information.

  • ”ID”: Information with only IDs.

  • ”META”: Metadata information.

  • ”SUMMARY”: Summary information (default).

• sortBy – Name of the property that the result list is sorted by.

Returns:

A DataFrame containing the list of cancer types.

Return type:

pandas.DataFrame

pybioportal.cancer_types.get_cancer_type(cancer_type_id)

Get a specific cancer type from cBioPortal.

Parameters:

cancer_type_id (str) – Cancer Type ID (e.g., “acc”).

Returns:

A DataFrame containing information about the specific cancer type.

Return type:

pandas.DataFrame

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Examples

from pybioportal import cancer_types as ct

df1 = ct.get_all_cancer_types()
df1

	name	dedicatedColor	shortName	parent	cancerTypeId
0	Aggressive Angiomyxoma	LightYellow	AA	soft_tissue	aa
1	Anaplastic Astrocytoma	Gray	AASTR	difg	aastr
2	Activated B-cell Type	LimeGreen	ABC	dlbclnos	abc
3	Acute Basophilic Leukemia	LightSalmon	ABL	amlnos	abl
4	Adrenocortical Adenoma	Purple	ACA	adrenal_gland	aca
...	...	...	...	...	...
880	Well-Differentiated Liposarcoma	LightYellow	WDLS	lipo	wdls
881	Well-Differentiated Thyroid Cancer	Teal	WDTC	thyroid	wdtc
882	Waldenstrom Macroglobulinemia	LimeGreen	WM	lpl	wm
883	Warty Penile Squamous Cell Carcinoma	Blue	WPSCC	pscc	wpscc
884	Wilms' Tumor	Orange	WT	kidney	wt

885 rows × 5 columns

df2 = ct.get_cancer_type(cancer_type_id="brca")
df2

	name	dedicatedColor	shortName	parent	cancerTypeId
0	Invasive Breast Carcinoma	HotPink	BRCA	breast	brca