Stabilised mosaic single cell data integration using unshared features

stabMapSE performs StabMap with SummarizedExperiment type (SingleCellExperiment, SpatialExperiment) objects as input.

stabMapSE(..., assays = "logcounts", args = list())

Arguments

...

Set of SummarizedExperiment, SingleCellExperiment, SpatialExperiment, etc that should be named.

assays

Named character vector of assays to be extracted from the objects.

args

List of arguments to be passed on to `stabMap`

Value

matrix containing common embedding with rows corresponding to cells, and columns corresponding to PCs or LDs for reference dataset(s).

Examples

set.seed(2021)
library(SingleCellExperiment)

sce_1 = SingleCellExperiment(assays = list(logcounts = mockMosaicData(names = "D1", ncells = 1000, ngenes = list(1:500))[[1]]))
sce_2 = SingleCellExperiment(assays = list(logcounts = mockMosaicData(names = "D2", ncells = 1000, ngenes = list(251:750))[[1]]))
sce_3 = SingleCellExperiment(assays = list(counts = mockMosaicData(names = "D3", ncells = 1000, ngenes = list(500:750))[[1]]))

out = stabMapSE(D1 = sce_1, D2 = sce_2)
#> treating "D1" as reference
#> generating embedding for path with reference "D1": "D1"
#> generating embedding for path with reference "D1": "D2" -> "D1"
#> treating "D2" as reference
#> generating embedding for path with reference "D2": "D2"
#> generating embedding for path with reference "D2": "D1" -> "D2"


# pass on additional parameters to stabMap()
# e.g. change number of components of reference
out = stabMapSE(D1 = sce_1, D2 = sce_2, args = list(ncomponentsReference = 20))
#> treating "D1" as reference
#> generating embedding for path with reference "D1": "D1"
#> generating embedding for path with reference "D1": "D2" -> "D1"
#> treating "D2" as reference
#> generating embedding for path with reference "D2": "D2"
#> generating embedding for path with reference "D2": "D1" -> "D2"

dim(out)
#> [1] 2000   40

# pull out different assay names:
out = stabMapSE(D2 = sce_2, D3 = sce_3, assays = c("D2" = "logcounts", "D3" = "counts"))
#> treating "D2" as reference
#> generating embedding for path with reference "D2": "D2"
#> generating embedding for path with reference "D2": "D3" -> "D2"
#> treating "D3" as reference
#> generating embedding for path with reference "D3": "D3"
#> generating embedding for path with reference "D3": "D2" -> "D3"