scib.metrics.graph_connectivity

scib.metrics.graph_connectivity(adata, label_key)

Graph Connectivity

Quantify the connectivity of the subgraph per cell type label. The final score is the average for all cell type labels \(C\), according to the equation:

\[GC = \frac {1} {|C|} \sum_{c \in C} \frac {|{LCC(subgraph_c)}|} {|c|}\]

where \(|LCC(subgraph_c)|\) stands for all cells in the largest connected component and \(|c|\) stands for all cells of cell type \(c\).

Parameters

• adata – adata with computed neighborhood graph

• label_key – name in adata.obs containing the cell identity labels