simba.tl.softmax

simba.tl.softmax(adata_ref, adata_query, T=0.5, n_top=None, percentile=0)[source]

Softmax-based transformation

This will transform query data to reference-comparable data

Parameters:

  • adata_ref (AnnData) – Reference anndata.

  • adata_query (list) – Query anndata objects

  • T (float) – Temperature parameter. 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.

  • cutoff (float) – The cutoff used to filter out low-probability reference entities

Returns:

  • updates adata_query with the following field.

  • softmax (array_like (.layers[‘softmax’])) – Store #observations × #dimensions softmax transformed data matrix.