UNAGI.UNAGI_analyst.analyst

class UNAGI.UNAGI_analyst.analyst(data_path, iteration, target_dir=None, customized_drug=None, cmap_dir=None, customized_mode=False)[source]

The analyst class is the class to perform downstream analysis. The analyst class will calculate the hierarchical markers, dynamic markers and perform the pathway and drug perturbations.

Parameters:

data_path (str) – the directory of the data (h5ad format, e.g. dataset.h5ad).
iteration (int) – the iteration used for analysis.
target_dir (str) – the directory to save the results. Default is None.
customized_drug (str) – the customized drug perturbation list. Default is None.
cmap_dir (str) – the directory to the cmap database. Default is None.

__init__(data_path, iteration, target_dir=None, customized_drug=None, cmap_dir=None, customized_mode=False)[source]

Methods

`__init__`(data_path, iteration[, target_dir, ...])
`perturbation_analyse_customized_drug`(...[, ...])	Perform perturbation on customized drug.
`perturbation_analyse_customized_pathway`(...)	Perform perturbation on customized pathway.
`start_analyse`(...)	Perform downstream tasks including dynamic markers discoveries, hierarchical markers discoveries, pathway perturbations and compound perturbations.