simba.tl.embed
- simba.tl.embed(adata_ref, list_adata_query, T=0.5, list_T=None, percentile=0, n_top=None, list_percentile=None, use_precomputed=False)[source]
Embed a list of query datasets along with reference dataset into the same space
- Parameters:
adata_ref (AnnData) – Reference anndata.
list_adata_query (list) – A list query anndata objects
T (float) – Temperature parameter shared by all query adata objects. It controls the output probability distribution. when T goes to inf, it becomes a discrete uniform distribution, each query becomes the average of reference; when T goes to zero, softargmax converges to arg max, each query is approximately the best of reference.
list_T (list, (default: None)) – A list of temperature parameters. It should correspond to each of query data. Once it’s specified, it will override T.
- Returns:
adata_all (AnnData) – Store #entities × #dimensions.
updates adata_query with the following field.
softmax (array_like (.layers[‘softmax’])) – Store #observations × #dimensions softmax transformed data matrix.