Sums the density columns of grouped cell types in each niche
reducedDim, producing coarser niche covariates (e.g. merging
Macrophage subtypes into a single "Macrophage" niche). Cell types absent from
groups are retained as their own (singleton) niche.
Usage
mergeNiches(spe, groups, ...)
# S4 method for class 'ANY'
mergeNiches(spe, groups, sigma = NULL, name = "Niche", ...)Arguments
- spe
a SpatialExperiment with niche reducedDims (see
buildNiches()).- groups
a named list mapping each merged niche name to a character vector of cell-type column names to sum.
- ...
ignored.
- sigma
a numeric vector of bandwidths to update;
NULL(default) updates everyname<sigma>reducedDim present.- name
a character, the reducedDim name prefix (default "Niche").
Details
The group membership is recorded in metadata(spe)$spiDE_niche_groups
so that a subsequent fitSpiDE() / nicheDesign() automatically excludes a
covariate whenever an index cell type is a member of the merged niche it is
tested against (its own density would otherwise contaminate the niche).
Examples
data(toySpiDE)
spe <- toySpiDE
spe <- buildNiches(spe, sigma = 20)
spe <- mergeNiches(spe, groups = list(AC = c("A", "C")), sigma = 20)
colnames(SingleCellExperiment::reducedDim(spe, "Niche20"))
#> [1] "AC" "B"