Deprecated: spatialData of subsets in ExperimentSubset objects

subsetSpatialData() and spatialData(x, subsetName =) are deprecated, and subsetSpatialData<- is defunct, because spatialData() and spatialData<- are deprecated in SpatialExperiment, which now keeps these columns in colData. Use subsetColData(x, subsetName) to get them, which returns all of the subset's colData columns, with parentColData = TRUE to include the main object's, and colData(x, subsetName = "name")$column <- values to add a column to a subset. The getters will be defunct in the next release.

Usage

subsetSpatialData(x, subsetName, parentSpatialData)

subsetSpatialData(x, subsetName) <- value

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

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

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

Arguments

x

ExperimentSubset Input ExperimentSubset object.

subsetName

character(1) Name of the subset to set spatialData to.

parentSpatialData

logical(1) Logical value indicating if parent spatialData should be combined or not. Default FALSE.

value

Ignored: the setter is defunct.

...

For spatialData(): subsetName and parentSpatialData, as for subsetSpatialData(). Without subsetName, all arguments are passed on to the SpatialExperiment method.

Value

The spatialData from input object, with a deprecation warning. The setter fails with an error.

See also

subsetColData