spateo.io.slideseq
==================

.. py:module:: spateo.io.slideseq

.. autoapi-nested-parse::

   IO functions for Slide-seq technology.



Attributes
----------

.. autoapisummary::

   spateo.io.slideseq.VERSIONS


Functions
---------

.. autoapisummary::

   spateo.io.slideseq.read_slideseq_as_dataframe
   spateo.io.slideseq.read_slideseq_beads_as_dataframe
   spateo.io.slideseq.read_slideseq


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

.. py:data:: VERSIONS

.. py:function:: read_slideseq_as_dataframe(path: str) -> pandas.DataFrame

   Read a Slide-seq digital expression matrix as long-format pandas DataFrame.

   :param path: Path to file

   :returns:

             Pandas DataFrame with the the following standardized column names.
                 * `barcode`: Bead barcode
                 * `gene`: Gene name/ID
                 * `count`: Observed UMIs. Zeros are filtered.


.. py:function:: read_slideseq_beads_as_dataframe(path: str) -> pandas.DataFrame

   Read a Slide-seq bead locations file.

   :param path: Path to file

   :returns:

             Pandas DataFrame with the following columns.
                 * `barcode`: Bead barcode
                 * `x`, `y`: X, Y coordinates


.. py:function:: read_slideseq(path: str, beads_path: str, binsize: Optional[int] = None, version: typing_extensions.Literal[slide2] = 'slide2') -> anndata.AnnData

   Read Slide-seq data as AnnData.

   :param path: Path to Slide-seq digital expression matrix CSV.
   :param beads_path: Path to CSV file containing bead locations.
   :param binsize: Size of pixel bins.
   :param version: Slideseq technology version. Currently only used to set the scale and
                   scale units of each unit coordinate. This may change in the future.