scanpy.read_10x_mtx

scanpy.read_10x_mtx(path, *, var_names='gene_symbols', make_unique=True, cache=False, cache_compression=_empty, gex_only=True, prefix=None, compressed=True)

Read 10x-Genomics-formatted mtx directory.

Parameters:

path PathLike[str] | str

Path to directory for .mtx and .tsv files, e.g. ‘./filtered_gene_bc_matrices/hg19/’.

var_names Literal['gene_symbols', 'gene_ids'] (default: 'gene_symbols')

The variables index.

make_unique bool (default: True)

Whether to make the variables index unique by appending ‘-1’, ‘-2’ etc. or not.

cache bool (default: False)

If False, read from source, if True, read from fast ‘h5ad’ cache.

cache_compression Union[Literal['gzip', 'lzf'], None, Empty] (default: _empty)

See the h5py Filter pipeline. (Default: settings.cache_compression)

gex_only bool (default: True)

Only keep ‘Gene Expression’ data and ignore other feature types, e.g. ‘Antibody Capture’, ‘CRISPR Guide Capture’, or ‘Custom’

prefix str | None (default: None)

Any prefix before matrix.mtx, genes.tsv and barcodes.tsv. For instance, if the files are named patientA_matrix.mtx, patientA_genes.tsv and patientA_barcodes.tsv the prefix is patientA_. (Default: no prefix)

compressed bool (default: True)

Whether to expect Cell Ranger v3+ files (.mtx, features.tsv, barcodes.tsv) to be gzipped. If True, ‘.gz’ suffix is appended to filenames. Set to False for STARsolo output. Has no effect on legacy (v2-) files.

Return type:

AnnData

Returns:

An AnnData object