SOAPy_st.pp.read_visium2adata

SOAPy_st.pp.read_visium2adata(path: str | PathLike, count_file: str = 'filtered_feature_bc_matrix.h5', filtered_feature_bc_matrix='filtered_feature_bc_matrix') → AnnData

Read spatial transcriptomics data of 10X Visium.

If an h5 file exists, the read_visium() method in scanpy is called by default, otherwise it is read through the filtered_feature_bc_matrix file.

filtered_feature_bc_matrix file need include:

features.tsv.gz; barcodes.tsv.gz; matrix.mtx.gz.

Parameters

path :

Path of Visium root directory folder.

count_file :

Which file in the passed directory to use as the count file. Typically either filtered_feature_bc_matrix.h5 or raw_feature_bc_matrix.h5.

filtered_feature_bc_matrix :

The folder containing the counts information in the root directory.

Returns

anndata.Anndata object