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Calculate graph connectivity per cell type

rs_graph_connectivity.Rd

[Experimental] For each cell type, the fraction of its cells in the largest connected component of the kNN graph restricted to that cell type. 1 means every cell type forms one connected piece. Edge direction is ignored.

Usage

rs_graph_connectivity(knn_mat, labels)

Arguments

knn_mat

Integer matrix. The rows represent the cells and the columns the neighbour indices (0-indexed!).

labels

Integer vector. The cell type per cell. The codes need not be 0-based or contiguous.

Value

A list with the following items

  • per_label - Connectivity per cell type, in order of first appearance in labels.

  • mean - Mean connectivity.

  • median - Median connectivity.

References

Luecken, et al., Nat Methods, 2022