Quadrat Analysis

Divides the tissue area into a grid and counts cells per quadrat. Tests for Complete Spatial Randomness using a chi-squared test.

Usage

QuadratAnalysis(object, nx = 5L, ny = 5L, target = NULL)

Arguments

object

An SpatialCellData-class object.

nx

Integer. Number of columns in the grid. Default 5.

ny

Integer. Number of rows in the grid. Default 5.

target

Character or NULL. Restrict to a phenotype.

Value

A list with counts, chi_sq, p_value, and VMR (variance-to-mean ratio).

Examples

counts <- matrix(rnorm(100), nrow = 50,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(50, 0, 100), y = runif(50, 0, 100))
obj <- CreateSpatialObject(counts, coords)
QuadratAnalysis(obj, nx = 3, ny = 3)
#> $counts
#>      [,1] [,2] [,3]
#> [1,]    5    3    5
#> [2,]    5    5    6
#> [3,]    8    2   11
#> 
#> $chi_sq
#> [1] 10.12
#> 
#> $p_value
#> [1] 0.2567043
#> 
#> $VMR
#> [1] 1.265
#>