Sketching: Downsampling and Geometric Sketching

In stevexniu/scMatchmaker: Single Cell Matchmaker

Downsampling and Geometric Sketching

Description

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

Usage

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

## Not run: 
object <- Sketching(object, size = 2000)

## End(Not run)

stevexniu/scMatchmaker documentation built on June 2, 2022, 12:35 p.m.