Downsampling and Geometric Sketching — Sketching • scMatchmaker

Run downsampling or geometric sketching to reduce number of cells for interaction calculation. See Hie et al. 2019 Cell Systems for details.

Sketching(
  object,
  cell_id = NULL,
  downsampling = TRUE,
  size = 2000,
  geom_pca_dims = 10,
  scale = TRUE,
  seed = 1,
  which_python = Sys.which(names = "python3")
)

Arguments

object: Matchmaker object.
cell_id: Cell IDs used to subset the data. Default is NULL. If provided the downsampling will be skipped.
downsampling: Perform downsampling based on the idents probability rather than geometric sketching. Default is TRUE.
size: Number of cells to return. Default is 2000. Please note that if downsampling is performed the actual size may vary due to rounding effect.
geom_pca_dims: Number of PCA dimensions to use. Default is 10.
scale: Whether to scale the data. Default is TRUE.
seed: Random seed number for sampling. Default is 1.
which_python: Path to python3 used.

Value

Returns a Matchmaker object.

Examples

if (FALSE) {
object <- Sketching(object, size = 2000)
}