Calculate manifold metrics — calc_manifold

This function will calculate the compactness and separation of your metacells on the manifold (defined by the diffusion map). You must have run calc_diffusion_coordinates() before calling this function. The idea is that compactness indicates how tight the metacell spans the manifold, whereas separation indicates how well the different metacells span the manifold.

Usage

calc_manifold_metrics(object)

Arguments

object: MetaCells class for which to calculate the different metrics.

Value

The class with the compactness and separation scores added.

References

Persad, et al. Nat Biotechnol, 2023

Examples

# compactness and separation on top of the diffusion coordinates
sc <- demo_single_cells()
mc <- generate_bt_meta_cells_sc(
  sc,
  sc_meta_cell_params = params_sc_bt_metacells(target_no_metacells = 50L),
  .verbose = FALSE
)
mc <- calc_diffusion_coordinates(
  mc,
  knn_data = get_knn_obj(sc),
  .verbose = FALSE
)
mc <- calc_manifold_metrics(mc)
head(mc[[c("compactness", "separation")]])
#>    compactness separation
#>          <num>      <num>
#> 1:  0.02674034 0.17462616
#> 2:  0.03287053 0.15380442
#> 3:  0.01897744 0.22679627
#> 4:  0.04910117 0.27503031
#> 5:  0.03481250 0.04071457
#> 6:  0.01309142 0.17024034

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