insitupy.InSituExperiment.from_config

insitupy.InSituExperiment.from_config#

classmethod InSituExperiment.from_config(config_path, mode='insitupy', **kwargs)#

Create an InSituExperiment object from a configuration file.

Parameters:

  • config_path (Union[str, os.PathLike, Path]) – The path to the configuration CSV or Excel file.

  • mode (Literal["insitupy", "xenium"], optional) – The mode to use for loading the datasets. Defaults to “insitupy”.

The configuration file should be either a CSV or Excel file (.csv, .xlsx, .xls) and must contain the following columns:

  • directory: This column is mandatory and should contain the paths to the directories where the datasets are stored. Each path should be a valid directory path.

  • Other columns: These columns can contain any additional metadata you want to associate with each dataset. The metadata will be extracted from these columns and stored in the InSituExperiment object.

Example of a valid configuration file:

directory

experiment_name

patient

treatment

/path/to/dataset1

Experiment 1

Patient A

Drug A

/path/to/dataset2

Experiment 2

Patient B

Drug B
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