tdm.raw.breast_mibi#

IMC breast-cancer dataset by The mibi file name is an early mistake in the codebase, it should be IMC. Danenberg et. al., Nature Genetics 2022 https://www.nature.com/articles/s41588-022-01041-y

Module Attributes

Downloading the MIBI data:

Functions

`all_image_numbers`()
`download_breast_mibi_data`()
`read_clinical_df`()	https://www.cbioportal.org/study/summary?id=brca_metabric
`read_single_cell_df`([ki67_threshold, ...])
`reassign_ki67_cluster`(single_cell_df)	Reassign each cell from the Ki67+ cluster to one of the cell types.

tdm.raw.breast_mibi.CELL_TYPE_DEFINITIONS_CD4_CD8_B = frozendict.frozendict({'Fibroblasts': 'F', 'Fibroblasts FSP1^{+}': 'F', 'Myofibroblasts PDPN^{+}': 'F', 'Myofibroblasts': 'F', 'Macrophages': 'M', 'Macrophages & granulocytes': 'M', 'CK^{med}ER^{lo}': 'Tu', 'CK^{+} CXCL12^{+}': 'Tu', 'CK8-18^{hi}ER^{lo}': 'Tu', 'CK8-18^{+} ER^{hi}': 'Tu', 'CK^{lo}ER^{lo}': 'Tu', 'CK8-18^{hi}CXCL12^{hi}': 'Tu', 'CK^{lo}ER^{med}': 'Tu', 'Endothelial': 'En', 'CD4^{+} T cells & APCs': 'CD4', 'CD4^{+} T cells': 'CD4', 'CD8^{+} T cells': 'CD8', 'B cells': 'B'})#: Downloading the MIBI data:

tdm.raw.breast_mibi.read_clinical_df()[source]#: https://www.cbioportal.org/study/summary?id=brca_metabric

tdm.raw.breast_mibi.read_single_cell_df(ki67_threshold: float = 0.5, cell_type_definitions: frozendict = frozendict.frozendict({'Fibroblasts': 'F', 'Fibroblasts FSP1^{+}': 'F', 'Myofibroblasts PDPN^{+}': 'F', 'Myofibroblasts': 'F', 'Macrophages': 'M', 'Macrophages & granulocytes': 'M', 'CK^{med}ER^{lo}': 'Tu', 'CK^{+} CXCL12^{+}': 'Tu', 'CK8-18^{hi}ER^{lo}': 'Tu', 'CK8-18^{+} ER^{hi}': 'Tu', 'CK^{lo}ER^{lo}': 'Tu', 'CK8-18^{hi}CXCL12^{hi}': 'Tu', 'CK^{lo}ER^{med}': 'Tu', 'Endothelial': 'En', 'CD4^{+} T cells & APCs': 'T', 'CD4^{+} T cells': 'T', 'CD8^{+} T cells': 'T', 'B cells': 'B'}), _reassign_ki67_cluster: bool = True) → DataFrame[source]#

tdm.raw.breast_mibi.reassign_ki67_cluster(single_cell_df: DataFrame) → DataFrame[source]#

Reassign each cell from the Ki67+ cluster to one of the cell types.

Parameters:: single_cell_df (pd.DataFrame) – the single-cell dataframe from Danenberg et. al 2022
Returns:: the single-cell dataframe with Ki67+ cells reassigned (in-place change)
Return type:: pd.DataFrame