Core function to conduct STADIA algorithm

core function to conduct STADIA algorithm

stadia(
  object.list,
  hyper,
  dim = 35,
  n_cluster = 7,
  platform = c("visium", "st", "others"),
  adj.cutoff = 50,
  icm.maxiter = 10,
  em.maxiter = 30,
  min.features = 200,
  min.spots = 20,
  nfeatures = 2000,
  verbose = TRUE,
  verbose.in = TRUE,
  ncores = NULL
)

Arguments

object.list

a list of seurat object.

hyper

a list of all hyperParameters.

dim

dimension of hidden space.

n_cluster

number of spatial domains.

platform

string vector to idicate platform generating data

adj.cutoff

cutoff when calculating adjacent matrix.

icm.maxiter

number of iteration of icm.

em.maxiter

number of iteration of em.

min.features

filtering low-quality data.

min.spots

filtering low-quality data.

nfeatures

number of HVGs.

verbose

print information or not.

verbose.in

print information or not.

ncores

number of cores to use.

Value

a list of estimated parameters.