dynamo.vf.torsion
- dynamo.vf.torsion(adata, basis='umap', vector_field_class=None, **kwargs)[source]
Calculate torsion for each cell with the reconstructed vector field function. AnnData object that is updated with the torsion key in the .obs.
- Parameters:
adata (
AnnData
) –AnnData
AnnData object that contains the reconstructed vector field function in the uns attribute.basis (
str
) – str or None (default: umap) The embedding data in which the vector field was reconstructed.vector_field_class (
Optional
[BaseVectorField
]) – dict The true ODE function, useful when the data is generated through simulation.kwargs – Any additional keys that will be passed to vector_field_class.compute_torsion function.
Examples
>>> adata = dyn.sample_data.hematopoiesis() >>> dyn.tl.reduceDimension(adata, n_components=3, enforce=True, embedding_key='X_umap_3d') >>> adata >>> dyn.tl.cell_velocities(adata, >>> X=adata.layers["M_t"], >>> V=adata.layers["velocity_alpha_minus_gamma_s"], >>> basis='umap_3d', >>> ) >>> dyn.vf.VectorField(adata, basis='umap_3d') >>> dyn.vf.torsion(adata, basis='umap_3d') >>> dyn.pl.streamline_plot(adata, color='torsion_umap_3d', basis='umap_3d') >>> dyn.pl.streamline_plot(adata, color='torsion_umap_3d')