skbio.table.Table.to_anndata#

Table.to_anndata(dense=False, dtype='float32', transpose=True)[source]#

Convert Table to AnnData format

Parameters:

densebool, optional: If True, set adata.X as np.ndarray instead of sparse matrix.
dtype: str, optional: dtype used for storage in anndata object.
tranpose: bool, optional: If True, transpose the anndata so that observations are columns

Returns:

anndata.AnnData: AnnData with matrix data and associated observation and sample metadata.

Notes

Nested metadata are not included.

Examples

>>> from biom import example_table
>>> adata = example_table.to_anndata()
>>> adata
AnnData object with n_obs × n_vars = 3 × 2
    obs: 'environment'
    var: 'taxonomy_0', 'taxonomy_1'