spateo.io.tenx#
IO functions for 10x Visium technology.
Module Contents#
Functions#
|
Read 10x Visium matrix directory as AnnData. |
|
Read 10x tissue positions CSV as dataframe. |
|
Read 10x Visium data as AnnData. |
Attributes#
- spateo.io.tenx.read_10x_as_anndata(matrix_dir: str) anndata.AnnData[source]#
Read 10x Visium matrix directory as AnnData.
- Parameters:
- matrix_dir
Path to directory containing matrix files.
- Returns:
AnnData of barcodes x genes.
- spateo.io.tenx.read_10x_positions_as_dataframe(path: str) pandas.DataFrame[source]#
Read 10x tissue positions CSV as dataframe. https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/images
- Parameters:
- path
Path to file
- Returns:
DataFrame containing barcode positions.
- spateo.io.tenx.read_10x(matrix_dir: str, positions_path: str, version: typing_extensions.Literal[visium] = 'visium') anndata.AnnData[source]#
Read 10x Visium data as AnnData.
- Parameters:
- matrix_dir
Directory containing matrix files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)
- positions_path
Path to CSV containing spatial coordinates
- version
10x technology version. Currently only used to set the scale and scale units of each unit coordinate. This may change in the future.