SpatialExperiment-colData: SpatialExperiment colData

In drighelli/VisiumExperiment: S4 Class for Spatially Resolved -omics Data

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

x	a SpatialExperiment
value	a DataFrame

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)

# 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)

drighelli/VisiumExperiment documentation built on April 10, 2024, 8:01 a.m.