squidpy.gr.sepal

squidpy.gr.sepal(adata, max_neighs, genes=None, n_iter=30000, dt=0.001, thresh=1e-08, connectivity_key='spatial_connectivities', spatial_key='spatial', layer=None, use_raw=False, copy=False, n_jobs=None, backend='loky', show_progress_bar=True)[source]

Identify spatially variable genes with Sepal.

Sepal is a method that simulates a diffusion process to quantify spatial structure in tissue. See [Anderson and Lundeberg, 2021] for reference.

Parameters
  • adata (AnnData) – Annotated data object.

  • max_neighs (Literal[4, 6]) –

    Maximum number of neighbors of a node in the graph. Valid options are:

    • 4 - for a square-grid (ST, Dbit-seq).

    • 6 - for a hexagonal-grid (Visium).

  • genes (Union[str, Sequence[str], None]) –

    List of gene names, as stored in anndata.AnnData.var_names, used to compute sepal score.

    If None, it’s computed anndata.AnnData.var ['highly_variable'], if present. Otherwise, it’s computed for all genes.

  • n_iter (Optional[int]) – Maximum number of iterations for the diffusion simulation. If n_iter iterations are reached, the simulation will terminate even though convergence has not been achieved.

  • dt (float) – Time step in diffusion simulation.

  • thresh (float) – Entropy threshold for convergence of diffusion simulation.

  • connectivity_key (str) – Key in anndata.AnnData.obsp where spatial connectivities are stored. Default is: anndata.AnnData.obsp ['spatial_connectivities'].

  • spatial_key (str) – Key in anndata.AnnData.obsm where spatial coordinates are stored.

  • layer (Optional[str]) – Layer in anndata.AnnData.layers to use. If None, use anndata.AnnData.X.

  • use_raw (bool) – Whether to access anndata.AnnData.raw.

  • copy (bool) – If True, return the result, otherwise save it to the adata object.

  • n_jobs (Optional[int]) – Number of parallel jobs.

  • backend (str) – Parallelization backend to use. See joblib.Parallel for available options.

  • show_progress_bar (bool) – Whether to show the progress bar or not.

Return type

Optional[DataFrame]

Returns

If copy = True, returns a pandas.DataFrame with the sepal scores.

Otherwise, modifies the adata with the following key:

Notes

If some genes in anndata.AnnData.uns ['sepal_score'] are NaN, consider re-running the function with increased n_iter.