pyXenium.multimodal.load_rna_protein_anndata#

load_rna_protein_anndata(base_path, *, prefer='auto', mex_dirname='cell_feature_matrix', mex_matrix_name='matrix.mtx.gz', mex_features_name='features.tsv.gz', mex_barcodes_name='barcodes.tsv.gz', cells_csv='cells.csv.gz', cells_parquet=None, read_morphology=False, attach_boundaries=True, clusters_relpath=DEFAULT_CLUSTER_RELPATH, cluster_column_name='cluster')#

Load a Xenium RNA + protein dataset into an AnnData object.

This is the canonical multimodal preparation entry point. It delegates all artifact parsing to pyXenium.io.read_xenium() and returns the aligned AnnData structure used by downstream joint RNA/protein analyses.

Parameters:

  • base_path (str)

  • prefer (str)

  • mex_dirname (str)

  • mex_matrix_name (str)

  • mex_features_name (str)

  • mex_barcodes_name (str)

  • cells_csv (str)

  • cells_parquet (str | None)

  • read_morphology (bool)

  • attach_boundaries (bool)

  • clusters_relpath (str | None)

  • cluster_column_name (str)

Return type:

AnnData