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Calculate the graph connectivity per cell type

calculate_graph_connectivity_sc.Rd

For each cell type, restricts the kNN graph to that cell type and takes the fraction of its cells in the largest connected component. A cell type split across batches after correction falls apart into several components and scores low. 1 means every cell type is one connected piece.

Usage

calculate_graph_connectivity_sc(object, cell_type_column, .verbose = TRUE)

Arguments

object

SingleCells or SingleCellsSubset class.

cell_type_column

String. The column with the cell type labels in the obs data of the class.

.verbose

Boolean. Controls verbosity of the function.

Value

A GraphConnectivityScores object with the following elements

  • per_cell_type - Named numeric. Connectivity per cell type.

  • mean_connectivity - Mean connectivity across cell types.

  • median_connectivity - Median connectivity across cell types.

References

Luecken, et al., Nat. Methods, 2022

Examples

# connectivity of each cell type in the kNN graph
sc <- demo_single_cells(
  syn_data_params = params_sc_synthetic_data(
    n_cells = 600L, n_genes = 50L, n_batches = 3L
  )
)
calculate_graph_connectivity_sc(sc, cell_type_column = "cell_grp")
#> Graph Connectivity
#>   Cell types: 3
#>   Mean:    1.0000 (1 = every cell type connected)
#>   Median:  1.0000
#>   Lowest:  cell_type_1 (1.000), cell_type_2 (1.000), cell_type_3 (1.000)

unlink(sc@dir_data, recursive = TRUE, force = TRUE)