RunGeomSketch: Run Geometric Sketching

In stevexniu/FuseNet: Non-Parametric Network Fusion

Run Geometric Sketching

Description

Run Geometric sketching sampling. See Hie et al. (doi: 10.1016/j.cels.2019.05.003) for details. This function relies on reticulate R package to import geosketch python library. Only one python environment is allowed by reticulate configuration. Please be careful when importing other R packages that will invoke and set up reticulate python configuration, i.e library(Seurat), before calling GeomSketch function.

Usage

RunGeomSketch(
  data,
  geom_size,
  is_pca = FALSE,
  n_pca = 10,
  seed = 1,
  which_python = Sys.which(names = "python3")
)

Arguments

data	An M x d matrix or data.frame with M rows of data points and d columns of features.
geom_size	Size of geometric sketches to return.
is_pca	Whether the data columns are principal components.
n_pca	Number of PCA dimensions to use. Default is 10.
seed	Random seed number. Default is 1.
which_python	Path to python3 used.

Value

Returns geometric sketch ID.

stevexniu/FuseNet documentation built on May 16, 2022, 12:23 p.m.