Get or set spatialCoords of subsets in ExperimentSubset objects

Get spatialCoords from a subset, with subsetSpatialCoords(x, subsetName) or spatialCoords(x, subsetName = ). Without subsetName, spatialCoords() returns the main object's, as for SpatialExperiment.

subsetSpatialCoords(x, subsetName) <- value stores a subset's own spatialCoords, for example after a transformation, without changing the main object's. A subset with its own coordinates returns them from subsetSpatialCoords(), spatialCoords(x, subsetName = ) and getSubsetExperiment(), and subsets made from it see them, cut to their spots. A subset without its own coordinates sees those of the nearest subset it was made from that has them, or else the main object's.

Usage

subsetSpatialCoords(x, subsetName)

subsetSpatialCoords(x, subsetName) <- value

# S4 method for class 'SubsetSpatialExperiment'
subsetSpatialCoords(x, subsetName)

# S4 method for class 'SubsetSpatialExperiment'
subsetSpatialCoords(x, subsetName) <- value

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

Arguments

x

ExperimentSubset Input ExperimentSubset object.

subsetName

character(1) Name of the subset to get spatialCoords from, or to store them in.

value

A numeric matrix with one row for each spot in the subset and one or more columns. Its rownames must be NULL or the subset's column names, in the same order. NULL removes the subset's own coordinates, so it sees those of the subset it was made from, or the main object's, again.

...

For spatialCoords():

subsetName

character(1) Name of the subset to get spatialCoords from. Leave it out for the main object's.

Without subsetName, all arguments are passed on to the SpatialExperiment method.

Value

For subsetSpatialCoords() and spatialCoords(), the spatialCoords the subset sees.

For subsetSpatialCoords<-, the input object with the subset's spatialCoords stored.

Examples

# a small SpatialExperiment with six spots
counts <- matrix(1:60, nrow = 10)
coords <- cbind(x = 1:6, y = 6:1)
spe <- SpatialExperiment(assays = list(counts = counts),
                         spatialCoords = coords)
es <- ExperimentSubset(spe)
es <- createSubset(es, "subset1", cols = 2:4)
subsetSpatialCoords(es, "subset1")
#>      x y
#> [1,] 2 5
#> [2,] 3 4
#> [3,] 4 3
# the same, through spatialCoords()
spatialCoords(es, subsetName = "subset1")
#>      x y
#> [1,] 2 5
#> [2,] 3 4
#> [3,] 4 3
# a small SpatialExperiment with six spots
counts <- matrix(1:60, nrow = 10)
coords <- cbind(x = 1:6, y = 6:1)
spe <- SpatialExperiment(assays = list(counts = counts),
                         spatialCoords = coords)
es <- ExperimentSubset(spe)
es <- createSubset(es, "subset1", cols = 2:4)
# store coordinates moved 100 to the right
movedCoords <- subsetSpatialCoords(es, subsetName = "subset1")
movedCoords[, "x"] <- movedCoords[, "x"] + 100
subsetSpatialCoords(es, subsetName = "subset1") <- movedCoords
subsetSpatialCoords(es, subsetName = "subset1")
#>        x y
#> [1,] 102 5
#> [2,] 103 4
#> [3,] 104 3
# the main object's coordinates are unchanged
spatialCoords(es)
#>      x y
#> [1,] 1 6
#> [2,] 2 5
#> [3,] 3 4
#> [4,] 4 3
#> [5,] 5 2
#> [6,] 6 1