czbenchmarks.datasets.single_cell_labeled
=========================================

.. py:module:: czbenchmarks.datasets.single_cell_labeled


Attributes
----------

.. autoapisummary::

   czbenchmarks.datasets.single_cell_labeled.logger


Classes
-------

.. autoapisummary::

   czbenchmarks.datasets.single_cell_labeled.SingleCellLabeledDataset


Module Contents
---------------

.. py:data:: logger

.. py:class:: SingleCellLabeledDataset(path: pathlib.Path, organism: czbenchmarks.datasets.types.Organism, label_column_key: str = 'cell_type', task_inputs_dir: Optional[pathlib.Path] = None)

   Bases: :py:obj:`czbenchmarks.datasets.single_cell.SingleCellDataset`


   Single cell dataset containing gene expression data and a label column.

   This class extends `SingleCellDataset` to include a label column that contains
   the expected prediction values for each cell. The labels are extracted from
   the specified column in `adata.obs` and stored as a `pd.Series` in the `labels`
   attribute.

   .. attribute:: labels

      Extracted labels for each cell.

      :type: pd.Series

   .. attribute:: label_column_key

      Key for the column in `adata.obs` containing the labels.

      :type: str

   Initialize a SingleCellLabeledDataset instance.

   :param path: Path to the dataset file.
   :type path: Path
   :param organism: Enum value indicating the organism.
   :type organism: Organism
   :param label_column_key: Key for the column in `adata.obs` containing the labels.
                            Defaults to "cell_type".
   :type label_column_key: str
   :param task_inputs_dir: Directory for storing task-specific inputs.
   :type task_inputs_dir: Optional[Path]


   .. py:attribute:: labels
      :type:  pandas.Series


   .. py:attribute:: label_column_key
      :type:  str


   .. py:method:: load_data() -> None

      Load the dataset and extract labels.

      This method loads the dataset using the parent class's `load_data` method
      and extracts the labels from the specified column in `adata.obs`.

      Populates:
          labels (pd.Series): Extracted labels for each cell.



   .. py:method:: store_task_inputs() -> pathlib.Path

      Store task-specific inputs, such as cell type annotations.

      This method stores the extracted labels in a JSON file. The filename is
      dynamically generated based on the `label_column_key`.

      :returns: Path to the directory storing the task input files.
      :rtype: Path