Geometric Sketching

Run Geometric sketching sampling. See Hie et al. (doi: 10.1016/j.cels.2019.05.003 ) for details.

GeomSketch(
  object,
  geom_size = 1000,
  geom_pca_dims = 10,
  sketch_n_pca = 0,
  sketch_k = 30,
  sketch_t = 0,
  geom_pca_seed = 1,
  which_python = Sys.which(names = "python3")
)

Arguments

object

A FuseNet object.

geom_size

Size of geometric sketches to return. Default is 1000.

geom_pca_dims

Number of PCA dimensions to use. Default is 10.

sketch_n_pca

Number of dimensions used for the sketched data points. Default is 0 and PCA is not performed. See details from InitiateFuseNet.

sketch_k

Number of nearest neighbors for the sketched data points. Default is 30. See details from InitiateFuseNet.

sketch_t

Matrix power used for the distance matrix. Default is 0 and powering is not performed. See details from InitiateFuseNet.

geom_pca_seed

Random seed number for PCA. Default is 1.

which_python

Path to python3 used.

Value

Returns a FuseNet object contains geometric sketch IDs.

Examples

if (FALSE) {
object <- GeomSketch(object, geom_size = 10)
}