Adds spatial differential expressed pattern (region-specific effects) to a cell type.

This function adds one type of spatial differential expressed patterns. This function can be repeated used to add region-specific effects in different regions for different cell types.

Usage

Add.Spatial.Expr.Pattern(
  sim.count,
  r,
  CellType,
  GeneID = NULL,
  PropOfGenes = 0.1,
  delta.mean = 1,
  delta.sd = 0.01,
  seed
)

Arguments

sim.count

Simulated expression counts from single-cell expression data, before adding in additional spatial patterns.

r

Which region to add in the spatial pattern.

CellType

Which cell type to add in the spatial pattern.

GeneID

Gene(s) index. Default = NULL, and then a random subset of genes will be perturbed based on the defined spatial patterns.

PropOfGenes

Proportion of genes with this pattern if GeneID is not provided.

delta.mean

Expected effect size (at the log scale of the counts).

delta.sd

Standard deviation of the effect size.

seed

Seed

Value

SignalSummary:

Summary of this spatial pattern, including the type of spatial patterns, impacted cell types, perturbed genes, and effect sizes.

beta.matrix:

Effect size on each gene in each cell.