spateo.io.tenx
==============

.. py:module:: spateo.io.tenx

.. autoapi-nested-parse::

   IO functions for 10x Visium technology.



Attributes
----------

.. autoapisummary::

   spateo.io.tenx.VERSIONS


Functions
---------

.. autoapisummary::

   spateo.io.tenx.read_10x_as_anndata
   spateo.io.tenx.read_10x_positions_as_dataframe
   spateo.io.tenx.read_10x


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

.. py:data:: VERSIONS

.. py:function:: read_10x_as_anndata(matrix_dir: str) -> anndata.AnnData

   Read 10x Visium matrix directory as AnnData.

   :param matrix_dir: Path to directory containing matrix files.

   :returns: AnnData of barcodes x genes.


.. py:function:: read_10x_positions_as_dataframe(path: str) -> pandas.DataFrame

   Read 10x tissue positions CSV as dataframe.
   https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/images

   :param path: Path to file

   :returns: DataFrame containing barcode positions.


.. py:function:: read_10x(matrix_dir: str, positions_path: str, version: typing_extensions.Literal[visium] = 'visium') -> anndata.AnnData

   Read 10x Visium data as AnnData.

   :param matrix_dir: Directory containing matrix files
                      (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)
   :param positions_path: Path to CSV containing spatial coordinates
   :param version: 10x technology version. Currently only used to set the scale and
                   scale units of each unit coordinate. This may change in the future.