spatial_clust: Main Spatial Clustering Method

In alexanderjwhite/spatialr.dev: Research, Development and Testing of Spatial Clustering Project

Main Spatial Clustering Method

Description

Main Spatial Clustering Method

Usage

spatial_clust(
  input,
  u_init,
  v_init,
  w = NULL,
  index = NULL,
  lambda = 1,
  cnorm = NULL,
  k = 20,
  epsilon = 0.001,
  maxiter = 1000
)

Arguments

input	SingleCellExperiment object containing counts assay and row/col coordinates.
u_init	matrix; u initialization matrix
v_init	matrix; v initialization matrix
w	matrix; distance matrix. If null, computed to specification with k nearest neighbors.
index	w index.
lambda	numeric; penalization parameter. set to NULL for lambda selection.
cnorm	a numeric value for the amount of V normalization. NULL for no normalization.
k	integer; if knn = TRUE, number of nearest neighbors to consider
epsilon	numeric; convergence criterion
maxiter	integer; maximum number of iterations

Value

Object containing u, v and convergence information

alexanderjwhite/spatialr.dev documentation built on Sept. 4, 2022, 4:49 a.m.