scanpy.read_10x_mtx

scanpy.read_10x_mtx(path, var_names='gene_symbols', make_unique=True, cache=False, gex_only=True)

Read 10x-Genomics-formatted mtx directory.

Parameters
path : Path, strUnion[Path, str]

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

var_names : {'gene_symbols', 'gene_ids'} (default: 'gene_symbols')

The variables index.

make_unique : boolbool

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

cache : boolbool

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

gex_only : boolbool

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

Return type

AnnDataAnnData

Returns

An AnnData object