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ingest

Map labels and embeddings from reference data to new data using specified labeling and embedding methods, supported by the SCMCP server for single-cell RNA sequencing analysis.

Instructions

Map labels and embeddings from reference data to new data

Input Schema

NameRequiredDescriptionDefault
embedding_methodNoEmbeddings in adata_ref which need to be mapped to adata. The only supported values are 'umap' and 'pca'.
labeling_methodNoThe method to map labels in adata_ref.obs to adata.obs. The only supported value is 'knn'.knn
neighbors_keyNoIf specified, ingest looks adata_ref.uns[neighbors_key] for neighbors settings and uses the corresponding distances.
obsNoLabels' keys in adata_ref.obs which need to be mapped to adata.obs (inferred for observation of adata).

Input Schema (JSON Schema)

{ "description": "Input schema for the ingest tool that maps labels and embeddings from reference data to new data.", "properties": { "embedding_method": { "anyOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "default": [ "umap", "pca" ], "description": "Embeddings in adata_ref which need to be mapped to adata. The only supported values are 'umap' and 'pca'.", "title": "Embedding Method" }, "labeling_method": { "default": "knn", "description": "The method to map labels in adata_ref.obs to adata.obs. The only supported value is 'knn'.", "title": "Labeling Method", "type": "string" }, "neighbors_key": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "If specified, ingest looks adata_ref.uns[neighbors_key] for neighbors settings and uses the corresponding distances.", "title": "Neighbors Key" }, "obs": { "anyOf": [ { "items": { "type": "string" }, "type": "array" }, { "type": "string" }, { "type": "null" } ], "default": null, "description": "Labels' keys in adata_ref.obs which need to be mapped to adata.obs (inferred for observation of adata).", "title": "Obs" } }, "title": "IngestModel", "type": "object" }

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