scanpy.tl.embedding_density

scanpy.tl.embedding_density(adata, basis='umap', *, groupby=None, key_added=None, components=None)

Calculate the density of cells in an embedding (per condition).

Gaussian kernel density estimation is used to calculate the density of cells in an embedded space. This can be performed per category over a categorical cell annotation. The cell density can be plotted using the pl.embedding_density function.

Note that density values are scaled to be between 0 and 1. Thus, the density value at each cell is only comparable to densities in the same category.

Beware that the KDE estimate used (scipy.stats.gaussian_kde) becomes unreliable if you don’t have enough cells in a category.

This function was written by Sophie Tritschler and implemented into Scanpy by Malte Luecken.

Parameters:

adata AnnData

The annotated data matrix.

basis str (default: 'umap')

The embedding over which the density will be calculated. This embedded representation should be found in adata.obsm['X_[basis]']`.

groupby str | None (default: None)

Key for categorical observation/cell annotation for which densities are calculated per category.

key_added str | None (default: None)

Name of the .obs covariate that will be added with the density estimates.

components str | Sequence[str] | None (default: None)

The embedding dimensions over which the density should be calculated. This is limited to two components.

Return type:

None

Returns:

Sets the following fields (key_added defaults to [basis]_density_[groupby], where [basis] is one of umap, diffmap, pca, tsne, or draw_graph_fa and [groupby] denotes the parameter input):

adata.obs[key_added]numpy.ndarray (dtype float)

Embedding density values for each cell.

adata.uns['[key_added]_params']dict

A dict with the values for the parameters covariate (for the groupby parameter) and components.

Examples

import scanpy as sc
adata = sc.datasets.pbmc68k_reduced()
sc.tl.umap(adata)
sc.tl.embedding_density(adata, basis='umap', groupby='phase')
sc.pl.embedding_density(
    adata, basis='umap', key='umap_density_phase', group='G1'
)

sc.pl.embedding_density(
    adata, basis='umap', key='umap_density_phase', group='S'
)

See also

pl.embedding_density