Returns the tidy per-(focal, neighbour) spatial variance table that
plotPairHeatmap() draws: for each focal cell type, the percentage of its
total expression variance contributed by spatial interaction with each
neighbour, obtained by splitting the focal's spatial share across neighbours
by a normalised (off-diagonal-renormalised) Pratt attribution. Off-diagonal
pairs only.
Usage
pairVariance(object, ...)
# S4 method for class 'PACEFit'
pairVariance(object, block = c("spatial", "responder"), ...)Arguments
- object
A PACEFit.
- ...
Unused.
- block
Either
"spatial"(default) or"responder"(condition cohorts).
Value
A data frame with columns focal, neighbour, and val (spatial %
of the focal type's total variance).
Examples
fit <- readRDS(system.file("extdata", "pace_fit_example.rds", package = "PACE"))
head(pairVariance(fit))
#> # A tibble: 6 × 3
#> focal neighbour val
#> <chr> <chr> <dbl>
#> 1 B_Cell Dendritic_Cell 0
#> 2 B_Cell Endothelial 0
#> 3 B_Cell Macrophage 0.00618
#> 4 B_Cell Myoepithelial 0
#> 5 B_Cell Stromal 0
#> 6 B_Cell T_Cell 2.73