terra.get_emd_distance

terra.get_emd_distance#

terra.get_emd_distance(dataset, model_folder_path, emb_layer=None, cell_gene_ensembl_id=[], neighborhood_gene_ensembl_id=[], batch_size=128, pin_memory=False, num_workers=12)#

Compute and return distance between cosine similarity of cell_neb and cell_cell matrix.

Parameters:

  • dataset (Dataset) – Tokenized Hugging Face dataset.

  • model_folder_path (str) – Path to the folder containing the model config, token dictionary, and normalization factors.

  • emb_layer (Optional[int] (default: None)) – Layer for which to retrieve the embedding.

  • cell_gene_ensembl_id (list (default: [])) – List with gene IDs for which cell gene embeddings will be retrieved.

  • neighborhood_gene_ensembl_id (list (default: [])) – List with gene IDs for which neighborhood gene embeddings will be retrieved.

  • batch_size (int (default: 128)) – Dataloader param.

  • pin_memory (bool (default: False)) – Dataloader param.

  • num_workers (int (default: 12)) – Number of workers used.

Return type:

ndarray

Returns:

-emd_array (ndarray)

Per-cell EMD distances, shape (n_cells,).

-emd_matrix (ndarray)

Per-cell gene-level distance matrix, shape (n_cells, n_genes).

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