Test for density correlation between two cell types.

Usage

corDensity(spe, coi = NULL, whole.slide = FALSE, probs = 0.85, trace = FALSE)

Arguments

spe: A SpatialExperiment object.
coi: Character vector for cell types of interest for density correlation analysis. Default is NULL, which is to consider all cell types previously calculated in the gridDensity() step.
whole.slide: Logical. Whether to compute correlation on all grids across the whole slide.
probs: A numeric scalar. The threshold of proportion that used to filter grids by density when ROIs have not been identified previously. Ignored if whole.slide is FALSE and 'roi' is present in the 'metadata' component of spe. Default to 0.85.
trace: Logical. If TRUE, print the process of testing. Default to FALSE.

Value

A DataFrame containing the testing results.

Examples


data("xenium_bc_spe")

coi <- c("Breast cancer", "Fibroblasts", "B cells", "T cells")

spe <- gridDensity(spe, coi = coi)

spe <- findROI(spe, coi = coi, method = "walktrap")

result <- corDensity(spe)