flowmap.utils.io ModuleΒΆ

Input/output helpers for saving FlowMap objects and moving metadata between FlowMap and AnnData.

from_embedder(embedder, adata=None, copy_layers=None, copy_obsm=None, copy_varm=None, copy_uns=False, metadata=None)

Wrap an existing fitted embedder in a FlowMapDataset. If adata is provided, selected single-cell metadata are copied into the wrapper.

Parameters

  • embedder: fitted VectorFieldEmbedder or compatible object with X and V.

  • adata: optional AnnData object used as the metadata source.

  • copy_layers: layer names to copy from adata.layers; use True to copy all.

  • copy_obsm: keys to copy from adata.obsm; use True to copy all.

  • copy_varm: keys to copy from adata.varm; use True to copy all.

  • copy_uns: copy adata.uns when True.

  • metadata: optional FlowMap-specific metadata.

Output

Returns a FlowMapDataset with the original object available as data.embedder.

from_anndata(adata, X_layer=None, V_layer="velocity", X_obsm=None, V_obsm=None, X_emb_obsm=None, V_emb_obsm=None, embedder=None, copy_layers=None, copy_obsm=None, copy_varm=None, copy_uns=False, metadata=None)

Create a FlowMapDataset directly from AnnData matrices and metadata.

Parameters

  • adata: AnnData-like object.

  • X_layer: optional layer key for the data matrix.

  • V_layer: layer key for the velocity matrix. Defaults to "velocity".

  • X_obsm: optional obsm key for the data matrix.

  • V_obsm: optional obsm key for the velocity matrix.

  • X_emb_obsm: optional obsm key copied as "X_flowmap".

  • V_emb_obsm: optional obsm key copied as "V_flowmap".

  • embedder: optional fitted FlowMap embedder to store on the dataset.

  • copy_layers: layer names to copy; use True to copy all.

  • copy_obsm: obsm keys to copy; use True to copy all.

  • copy_varm: varm keys to copy; use True to copy all.

  • copy_uns: copy adata.uns when True.

  • metadata: optional FlowMap-specific metadata.

Output

Returns a FlowMapDataset.

to_anndata(data)

Convert a FlowMapDataset back to an AnnData object.

Parameters

  • data: FlowMapDataset instance.

Output

Returns an AnnData object. If data.X is reduced feature space but data.var describes genes, the original var table is stored under adata.uns["flowmap"].

save_dataset(data, path, **joblib_kwargs)

Save a FlowMapDataset as a regular .joblib file.

Parameters

  • data: FlowMapDataset instance.

  • path: output path.

  • joblib_kwargs: additional keyword arguments passed to joblib.dump.

Output

Returns None.

load_dataset(path)

Load a FlowMapDataset saved with save_dataset.

Parameters

  • path: input .joblib path.

Output

Returns a FlowMapDataset.

save_embedder(embedder, path, **joblib_kwargs)

Save a fitted embedder as a regular .joblib file.

Parameters

  • embedder: fitted VectorFieldEmbedder or compatible object.

  • path: output path.

  • joblib_kwargs: additional keyword arguments passed to joblib.dump.

Output

Returns None.

load_embedder(path)

Load a fitted embedder saved with save_embedder.

Parameters

  • path: input .joblib path.

Output

Returns the loaded Python object.