Skip to contents

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

Source: R/ExprSimulator.R
Pattern.Adj.Rd

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
)

Arguments

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 10% of the total counts across all genes.

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).

Value

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