Notebook 03 batch -> wrap_batch_evaluation -> calculate LISI
Running wrap_batch_evaluation(batch_corrections, batch_key=batch_column, threads=threads, inplace=True) runs into
Expected n_neighbors <= n_samples, but n_samples = 48, n_neighbors = 90 in cases of small sample numbers, suchs as given when using the notebooks for bulk datasets
90 seems to be hard coded somewhere
Solution: add perplexity as a parameter to wrap_batch_evaluation() and add it to job = pool.apply_async(compute_lisi, args=(obsm_matrix, obs_mat, [batch_key], perplexity)) call --> n_neighbors seems to be set by 3* perplexity value
Set perplexity in dependency of n_samples by (n_namples) /3 -1 or smaller