dynamo.vf.diffusionMatrix
- dynamo.vf.diffusionMatrix(adata, X_data=None, V_data=None, genes=None, layer=None, basis='umap', dims=None, n=30, VecFld=None, residual='vector_field')[source]
Calculate the diffusion matrix from the estimated velocity vector and the reconstructed vector field.
- Parameters:
adata (
AnnData) – an Annodata object.X_data (
Optional[ndarray]) – The user supplied expression (embedding) data that will be used for calculating diffusion matrix directly.V_data (
Optional[ndarray]) – The user supplied velocity data that will be used for calculating diffusion matrix directly.genes (
Optional[List]) – The list of genes that will be used to subset the data. If None, all genes will be used.layer (
Optional[str]) – Which layer of the data will be used for diffusion matrix calculation.basis (
str) – Which basis of the data will be used for diffusion matrix calculation.dims (
Optional[List]) – The list of dimensions that will be selected for diffusion matrix calculation. If None, all dimensions will be used.n (
int) – Number of nearest neighbors when the nearest neighbor graph is not included.VecFld (
Optional[VecFldDict]) – The reconstructed vector field function.residual (
str) – Method to calculate residual velocity vectors for diffusion matrix calculation. If average, all velocity of the nearest neighbor cells will be minused by its average velocity; if vector_field, all velocity will be minused by the predicted velocity from the reconstructed deterministic velocity vector field.
- Returns:
- AnnData object that is updated with the diffusion_matrix key in the uns attribute which is a list of
the diffusion matrix for each cell. A column diffusion corresponds to the square root of the sum of all elements for each cell’s diffusion matrix will also be added.
- Return type:
adata