Reduced dimensions of subsets in ExperimentSubset objects

Get or set the reduced dimensions, such as a PCA or UMAP, of a subset by naming it with subsetName. Without subsetName, these methods act on the main object, as for SingleCellExperiment. They exist for the classes that extend SingleCellExperiment: SubsetSingleCellExperiment, SubsetSpatialExperiment and SubsetTreeSummarizedExperiment. reducedDimNames and reducedDimNames<- have their own pages.

Usage

# S4 method for class 'SubsetSingleCellExperiment,character'
reducedDim(x, type, ...)

# S4 method for class 'SubsetSingleCellExperiment,missing'
reducedDim(x, type, ...)

# S4 method for class 'SubsetSingleCellExperiment,numeric'
reducedDim(x, type, ...)

# S4 method for class 'SubsetSingleCellExperiment,character'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment,missing'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment,numeric'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSingleCellExperiment'
reducedDims(x, ...)

# S4 method for class 'SubsetSingleCellExperiment'
reducedDims(x, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSpatialExperiment,character'
reducedDim(x, type, ...)

# S4 method for class 'SubsetSpatialExperiment,missing'
reducedDim(x, type, ...)

# S4 method for class 'SubsetSpatialExperiment,numeric'
reducedDim(x, type, ...)

# S4 method for class 'SubsetSpatialExperiment,character'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSpatialExperiment,missing'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSpatialExperiment,numeric'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetSpatialExperiment'
reducedDims(x, ...)

# S4 method for class 'SubsetSpatialExperiment'
reducedDims(x, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment,character'
reducedDim(x, type, ...)

# S4 method for class 'SubsetTreeSummarizedExperiment,missing'
reducedDim(x, type, ...)

# S4 method for class 'SubsetTreeSummarizedExperiment,numeric'
reducedDim(x, type, ...)

# S4 method for class 'SubsetTreeSummarizedExperiment,character'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment,missing'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment,numeric'
reducedDim(x, type, withDimnames = TRUE, ...) <- value

# S4 method for class 'SubsetTreeSummarizedExperiment'
reducedDims(x, ...)

# S4 method for class 'SubsetTreeSummarizedExperiment'
reducedDims(x, withDimnames = TRUE, ...) <- value

Arguments

x

An ExperimentSubset object.

type

character(1) or integer(1) The name or position of the reduced dimension. Leave it out for the first one.

...

subsetName

character(1) Name of the subset whose reduced dimensions to get or set. Leave it out for the main object's. Give it by name: for reducedDims<-, a subset name in second place is withDimnames, and an error.

Other arguments are passed on to the SingleCellExperiment method, for the subset or the main object.

withDimnames

logical(1) Passed on to reducedDim<- or reducedDims<-. Default TRUE.

value

For reducedDim<-, a matrix with one row per column of the subset (or of the main object). For reducedDims<-, a named list of such matrices, which replaces all of them.

Value

reducedDim() returns a matrix and reducedDims() a list of them. reducedDim<- and reducedDims<- return x with the reduced dimensions stored.

See also

reducedDims

Examples

# an object with 10 genes and 20 cells
set.seed(1)
counts <- matrix(rpois(200, lambda = 5), nrow = 10)
rownames(counts) <- paste0("gene", 1:10)
colnames(counts) <- paste0("cell", 1:20)
es <- ExperimentSubset(list(counts = counts))
# a subset of the first 5 genes and the first 8 cells
es <- createSubset(es, subsetName = "first", rows = 1:5, cols = 1:8)
# a 2-dimensional embedding of the subset's 8 cells
embedding <- matrix(rnorm(16), ncol = 2)
# store it in the subset
reducedDim(es, "PCA", subsetName = "first") <- embedding
# read it back
reducedDim(es, "PCA", subsetName = "first")
#>              [,1]       [,2]
#> cell1 -0.62036668  0.3841854
#> cell2  0.04211587  1.6821761
#> cell3 -0.91092165 -0.6357365
#> cell4  0.15802877 -0.4616447
#> cell5 -0.65458464  1.4322822
#> cell6  1.76728727 -0.6506964
#> cell7  0.71670748 -0.2073807
#> cell8  0.91017423 -0.3928079
# all of the subset's reduced dimensions
reducedDims(es, subsetName = "first")
#> List of length 1
#> names(1): PCA
# replace them all with a list of two
reducedDims(es, subsetName = "first") <- list(PCA = embedding,
                                              UMAP = embedding * 2)
reducedDimNames(es, subsetName = "first")
#> [1] "PCA"  "UMAP"