phlower.tl.branch_regulator_detect
- phlower.tl.branch_regulator_detect(adata: AnnData, tfadata: AnnData, branch, tree='fate_tree', tree_attr='original', ratio=0.5, intersect_regulator=60, vs_name='auto', log2fc='auto', correlation='auto')
Encapsulate the step of regulator finding 1. specify an end branch name, automatically decide the comparison branch/branches 2. perform differentation between two branches 3. select top markers
Parameters
- adata: AnnData
the data object
- tfadata: AnnData
the data object of transcription factors
- branch: str
the end branch name
- tree: str
the fate tree name
- tree_attr: str
the fate tree attribute
- ratio: float
the ratio of cells in the branch to be selected
- intersect_regulator: int
the number of intersected regulators from differentiation or correlations
- vs_name: str
the name of the comparison branch default: {tree}_level_{branch}
- log2fc: Union[str, float]
the log2fc cutoff for differentiation default: “auto”
- correlation: Union[str, float]
the correlation cutoff for correlation default: “auto”