API

API#

The main user-facing API is exposed at the top level of the terra package. The typical workflow is to harmonize an AnnData, tokenize it against a trained model, and embed it:

from terra import download_pretrained, harmonize_tokenize_embed_pipeline

Inference#

harmonize_tokenize_embed_pipeline(adata, ...)

Harmonize, tokenize and embed an AnnData object.

harmonize_adata(adata[, ...])

Harmonize an AnnData object prior to tokenization.

tokenize_adata(adata, model_folder_path, ...)

Harmonize and tokenize an AnnData object based on the parameters in the model config and return the tokenized Hugging Face dataset and harmonized AnnData object.

embed_dataset(dataset, model_folder_path[, ...])

Embed a tokenized dataset, returning cell-, neighborhood- and gene-level embeddings.

gene_embed_dataset(dataset, model_folder_path)

Compute per-gene cell and neighborhood embeddings (and optional cosine-similarity / EMD statistics) over a tokenized dataset.

infer(args, dataset, load_folder_path[, ...])

Use a trained model for inference.

get_gene_embed(dataset, model_folder_path[, ...])

Retrieve gene embeddings for specified cell and neighborhood gene IDs.

get_average_gene_embed(dataset, ...[, ...])

Retrieve average gene embeddings for each gene per dataset.

perturb_dataset(dataset, perturb_df, ...[, ...])

Perturb a tokenized Hugging Face dataset according to a perturbation dataframe.

get_emd_distance(dataset, model_folder_path)

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

get_spatial_score(dataset, model_folder_path)

Compute and return cosine similarity matrix for specified gene IDs.

Hugging Face Hub#

download_pretrained(repo_id, *[, revision, ...])

Download a published TERRA model bundle.

push_model_to_hub(model_folder, repo_id, *)

Create (if needed) a Hugging Face model repo and upload a TERRA model bundle.

Data#

Convenience reader used by the tutorials to load public 10x Genomics Xenium samples.

read_xenium_10x(base_url, out_dir)

Download a 10x Genomics Xenium sample and load it as an AnnData.
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