%matplotlib inline
Neighbors enrichment analysis
This example shows how to run the neighbors enrichment analysis routine.
It calculates an enrichment score based on proximity on the connectivity graph of cell clusters. The number of observed events is compared against \(N\) permutations and a z-score is computed.
See also
See {doc}`compute_spatial_neighbors` for general usage of
{func}`squidpy.gr.spatial_neighbors`.
import squidpy as sq
adata = sq.datasets.visium_fluo_adata()
adata
AnnData object with n_obs × n_vars = 2800 × 16562
obs: 'in_tissue', 'array_row', 'array_col', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_MT', 'log1p_total_counts_MT', 'pct_counts_MT', 'n_counts', 'leiden', 'cluster'
var: 'gene_ids', 'feature_types', 'genome', 'MT', 'n_cells_by_counts', 'mean_counts', 'log1p_mean_counts', 'pct_dropout_by_counts', 'total_counts', 'log1p_total_counts', 'n_cells', 'highly_variable', 'highly_variable_rank', 'means', 'variances', 'variances_norm'
uns: 'cluster_colors', 'hvg', 'leiden', 'leiden_colors', 'neighbors', 'pca', 'spatial', 'umap'
obsm: 'X_pca', 'X_umap', 'spatial'
varm: 'PCs'
obsp: 'connectivities', 'distances'
This dataset contains cell type annotations in anndata.Anndata.obs
which are used for calculation of the
neighborhood enrichment. First, we need to compute a connectivity matrix from spatial coordinates.
sq.gr.spatial_neighbors(adata)
Then we can calculate the neighborhood enrichment score with squidpy.gr.nhood_enrichment()
.
sq.gr.nhood_enrichment(adata, cluster_key="cluster")
And visualize the results with squidpy.pl.nhood_enrichment()
.
sq.pl.nhood_enrichment(adata, cluster_key="cluster")