sc_utils.write_mtx

sc_utils.write_mtx(adata, output_dir)[source]

Save scanpy object in mtx cellranger v3 format.

Saves basic information from adata object as cellranger v3 mtx folder. Saves only adata.var_names, adata.obs_names and adata.X fields. Creates directory output_dir if it does not exist. Creates 3 files: features.tsv.gz, barcodes.tsv.gz and matrix.mtz.gz. Will overwrite files in the output directory.

Parameters

  • adata – Annotated data matrix.

  • output_dir – Directory where to save results