glue_genes.glue_single_cell.anndata_factory.read_anndata

glue_genes.glue_single_cell.anndata_factory.read_anndata(file_name, skip_dialog=False, skip_components=[], subsample=False, subsample_factor=1, try_backed=False)

Use AnnData to read a single-cell type data file into three linked glue Data objects.

AnnData objects are mapped into three glue Data objects that are linked by JoinLink

Currently supports .h5ad and .loom files, but reading in backed mode is only supported for .h5ad because of underlying limitations with AnnData.

Parameters:

file_name: str

The file to read

skip_dialog: bool, optional

Whether to skip the GUI module (useful for scripts and testing)

skip_components: list, optional

The names of columns in obs/var/obsm/varm to NOT load

subsample: bool, optional

Whether to subsample on obs to reduce file size

subsample_factor: int, optional

If specified, and subsample, reduce the size of obs by this factor

try_backed: bool, optional

Attempt to use disk-based access to the data. If AnnData fails to load the file this way it will be loaded into memory.