spateo.io.seqscope#
IO functions for SeqScope technology.
Module Contents#
Functions#
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Read SeqScope matrix directory as AnnData. |
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Read SeqScope barcode positions CSV as dataframe. |
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Read SeqScope data as AnnData. |
- spateo.io.seqscope.read_seqscope_as_anndata(matrix_dir: str) anndata.AnnData[source]#
Read SeqScope matrix directory as AnnData.
- Parameters:
- matrix_dir
Path to directory containing matrix files.
- Returns:
AnnData of barcode x genes.
- spateo.io.seqscope.read_seqscope_positions_as_dataframe(path: str) pandas.DataFrame[source]#
Read SeqScope barcode positions CSV as dataframe.
- Parameters:
- path
Path to file
- Returns:
DataFrame containing barcode positions.
- spateo.io.seqscope.read_seqscope(matrix_dir: str, positions_path: str, binsize: int | None = 1, add_props: bool = True, version: Literal[seqscope] = 'seqscope') anndata.AnnData[source]#
Read SeqScope 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
- binsize
Size of pixel bins
- add_props
Whether or not to compute label properties, such as area, bounding box, centroid, etc.
- version
SeqScope technology version. Currently only used to set the scale and scale units of each unit coordinate. This may change in the future.