Add cell-cell expr-expr interaction pattern to a pair of cell types

This function add cell-cell interactions to a pair of cell types (e.g. neuron-microglia) for expression in a cell type associated with expression of the neighboring other cell type. One can repeat this function for multiple times to add cell-cell interactions for many cell types.

Usage

Add.Expr.Asso.Pattern(
  ppp.obj,
  sim.count,
  r,
  perturbed.cell.type,
  adjacent.cell.type,
  Bidirectional = T,
  int.dist.threshold = 0.1,
  delta.mean = 1,
  delta.sd = 0.001,
  GenePairIDMatrix = NULL,
  PropOfGenes = NULL,
  seed = NULL
)

Arguments

ppp.obj

An object of class "ppp" representing simulated cell locations

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. If simulated data do not have multiple regions, r=1.

perturbed.cell.type

Which cell type is perturbed from this cell-cell interaction (e.g. microglia).

adjacent.cell.type

Which cell type in the neighbor perturbs from the cell-cell interaction (e.g. neuron).

Bidirectional

Whether the perturbation is both directional.

int.dist.threshold

The minimal cell-cell distance for the interaction.

delta.mean

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

delta.sd

Standard deviation of the effect.size

GenePairIDMatrix

Affected gene pairs.

PropOfGenes

Proportion of genes impacted by the cell-cell interaction. It is used if GenePairIDMatrix is NULL, and a random subset of genes with specified proportion will be perturbed.

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.