simba.tl.compare_entities
- simba.tl.compare_entities(adata_ref, adata_query, n_top_cells=50, T=1)[source]
Compare the embeddings of two entities by calculating
the following values between reference and query entities:
dot product
normalized dot product
softmax probability
and the following metrics for each query entity:
max (The average maximum dot product of top-rank reference entities, based on normalized dot product)
std (standard deviation of reference entities, based on dot product)
gini (Gini coefficients of reference entities, based on softmax probability)
entropy (The entropy of reference entities, based on softmax probability)
- Parameters:
adata_ref (AnnData) – Reference entity anndata.
adata_query (list) – Query entity anndata.
n_top_cells (int, optional (default: 50)) – The number of cells to consider when calculating the metric ‘max’
T (float) – Temperature parameter for softmax. 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.
- Returns:
adata_cmp – Store reference entity as observations and query entity as variables
- Return type:
AnnData