SpatialExperiment colData

Description

The SpatialExperiment class provides a modified colData setter, which ensures that the SpatialExperiment object remains valid.

Usage

## S4 replacement method for signature 'SpatialExperiment,DataFrame'
colData(x) <- value

## S4 replacement method for signature 'SpatialExperiment,'NULL''
colData(x) <- value

Arguments

Details

The colData setter performs several checks to ensure validity. If the replacement colData does not contain a sample_id column, the existing sample_ids will be retained. If the replacement colData contains sample_ids, a check is performed to ensure the number of unique sample_ids is the same, i.e. a one-to-one mapping is possible. If the replacement is NULL, the sample_ids are retained. In addition, checks are performed against the sample_ids in imgData.

Value

a SpatialExperiment object with updated colData

Examples

example(read10xVisium)
colData(spe) <- NULL