Adjust the count data for all cells in all regions based on the input spatial patterns

Adjust the count data for all regions based on the input spatial patterns

Usage

Pattern.Adj(
  sim.count,
  pattern.list = NULL,
  bond.extreme = T,
  keep.total.count = F,
  integer = T
)

sim.count: Spatial info for cell type 1 (e.g. neuron)
pattern.list: A list of spatial patterns, which can be generated from Add.Spatial.Expr.Pattern, Add.Distance.Asso.Pattern, or Add.Expr.Asso.Pattern.
bond.extreme: Whether to bond extreme high values generated from large effect sizes of spatial patterns (default = TRUE). If TRUE, no gene can have more than the maximum of (1) 5 times the 97.5 percentile of the pattern adjusted count and (2) the maximum of the original count.
keep.total.count: If additional spatial patterns are added, whether to rescale expression levels of all genes to keep the sequencing depth (default = FALSE).
integer: Whether to keep counts as integer (default=TRUE).

Updated simulated gene expression counts by taking into consideration of spatial patterns.