plotInterCellTypeSpatialCrossCor: Expression correlation between cells of group A expressing...

In JEFworks/MERingue: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities

Expression correlation between cells of group A expressing gene A with neighbors of cells of group A in group B expressing gene B

Description

Expression correlation between cells of group A expressing gene A with neighbors of cells of group A in group B expressing gene B

Usage

plotInterCellTypeSpatialCrossCor(
  gexpA,
  gexpB,
  groupA,
  groupB,
  weight,
  fun = mean,
  ...
)

Arguments

gexpA	Expression of gene A
gexpB	Expression of gene B
groupA	Cells of group A
groupB	Cells of group B
weight	Adjacency weight matrix
fun	Function for combining multiple gene expression values (ex. mean, median, max)
...	Additional plotting parameters

Value

None

Examples

# Simulate data
set.seed(0)
N <- 100
pos <- cbind(rnorm(N), rnorm(N))
rownames(pos) <- paste0('cell', 1:N)
colnames(pos) <- c('x', 'y')
weight <- getSpatialNeighbors(pos)
ctA <- sample(rownames(pos), N/2)
ctB <- setdiff(rownames(pos), ctA)
gexpA <- pos[,2]
gexpA[ctB] <- 0
gexpB <- -pos[,2]
gexpB[ctA] <- 0
plotEmbedding(pos, col=gexpA)
plotEmbedding(pos, col=gexpB)
plotInterCellTypeSpatialCrossCor(gexpA, gexpB, ctA, ctB, weight)
plotInterCellTypeSpatialCrossCor(gexpB, gexpA, ctB, ctA, weight)

JEFworks/MERingue documentation built on June 11, 2022, 4:16 a.m.