maxfuse.utils.process_count_data

maxfuse.utils.process_count_data(arr, target_sum=1e4, min_mean=0.0125, max_mean=3, min_disp=0.5, max_value=10)[source]

Process count data according to scanpy pipeline.

Parameters:

  • arr (np.array of shape (n_samples, n_features)) – Data matrix

  • target_sum (float, default=1e4) – Parameter in sc.pp.normalize_total

  • min_mean (float, default=0.0125) – Parameter in sc.pp.higly_variable_genes

  • max_mean (float, default=3) – Parameter in sc.pp.higly_variable_genes

  • min_disp (float, default=0.5) – Parameter in sc.pp.higly_variable_genes

  • max_value (float, default=10) – Parameter in sc.pp.scale

Returns:

An np.array representing the processed version of arr