SpatialExperiment-colData {SpatialExperiment} | R Documentation |
The SpatialExperiment
class provides a modified colData
setter, which ensures that the SpatialExperiment
object remains valid.
## S4 replacement method for signature 'SpatialExperiment,DataFrame' colData(x) <- value ## S4 replacement method for signature 'SpatialExperiment,'NULL'' colData(x) <- value
x |
|
value |
The colData
setter performs several checks to ensure validity. If the
replacement colData
does not contain a sample_id
column, the
existing sample_id
s will be retained. If the replacement
colData
contains sample_id
s, a check is performed to ensure the
number of unique sample_id
s is the same, i.e. a one-to-one mapping is
possible. If the replacement is NULL
, the sample_id
s are
retained. In addition, checks are performed against the sample_id
s in
imgData
.
a SpatialExperiment
object with updated colData
example(read10xVisium) # return additional columns for colData head(colData(spe, spatialData = TRUE, spatialCoords = TRUE)) # empty replacement retains sample identifiers colData(spe) <- NULL names(colData(spe)) # replacement of sample identifiers # requires one-to-one mapping ## invalid replacement tryCatch( spe$sample_id <- seq(ncol(spe)), error = function(e) message(e)) ## valid replacement old <- c("section1", "section2") new <- c("sample_A", "sample_B") idx <- match(spe$sample_id, old) tmp <- spe tmp$sample_id <- new[idx] table(spe$sample_id, tmp$sample_id)