use the compare_entities method to assess 'closeness' of embedded elements

compare_entities(simbaref, refemb, queryemb, n_top = 50L, temperature = 1)

Arguments

simbaref: instance of python module for simba
refemb: AnnData instance with 'reference' embedding
queryemb: AnnData instance with 'query' embedding
n_top: integer(1) number of 'reference' elements to be examined for 'max' output summarizing closeness (maximum of normed dot product)
temperature: numeric(1), a tuning parameter whose reciprocal scales softmax transformations of dot products between reference and query entities, defaulting to 1.0 for this application

Examples

  simbaref = simba_ref()
  cemb = simbaref$read_h5ad( get_3k_cell_emb() )
  gemb = simbaref$read_h5ad( get_3k_gene_emb() )
  cc = compare_entities( simbaref, cemb, gemb )
#> Error in eval(cl, parent.frame()): object 'cemb' not found
  cc
#> Error in eval(expr, envir, enclos): object 'cc' not found
  head(cc$var)
#> Error in eval(expr, envir, enclos): object 'cc' not found