The SpatialExperiment class provides a modified colData
setter, which ensures that the SpatialExperiment object remains valid.
Usage
# S4 method for class 'SpatialExperiment,DataFrame'
colData(x) <- value
# S4 method for class 'SpatialExperiment,`NULL`'
colData(x) <- valueValue
a SpatialExperiment object with updated colData
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.
Examples
example(read10xVisium)
#>
#> rd10xV> dir <- system.file(
#> rd10xV+ file.path("extdata", "10xVisium"),
#> rd10xV+ package = "SpatialExperiment")
#>
#> rd10xV> sample_ids <- c("section1", "section2")
#>
#> rd10xV> samples <- file.path(dir, sample_ids, "outs")
#>
#> rd10xV> list.files(samples[1])
#> [1] "raw_feature_bc_matrix" "spatial"
#>
#> rd10xV> list.files(file.path(samples[1], "spatial"))
#> [1] "scalefactors_json.json" "tissue_lowres_image.png"
#> [3] "tissue_positions_list.csv"
#>
#> rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
#> [1] "/tmp/RtmppdZi9A/temp_libpathcf263c794d1/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"
#>
#> rd10xV> (spe <- read10xVisium(samples, sample_ids,
#> rd10xV+ type = "sparse", data = "raw",
#> rd10xV+ images = "lowres", load = FALSE))
#> class: SpatialExperiment
#> dim: 50 99
#> metadata(0):
#> assays(1): counts
#> rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
#> ENSMUSG00000005886 ENSMUSG00000101476
#> rowData names(1): symbol
#> colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
#> AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1
#> colData names(4): in_tissue array_row array_col sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(4): sample_id image_id data scaleFactor
#>
#> rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
#> rd10xV> samples2 <- file.path(dir, sample_ids)
#>
#> rd10xV> (spe2 <- read10xVisium(samples2, sample_ids,
#> rd10xV+ type = "sparse", data = "raw",
#> rd10xV+ images = "lowres", load = FALSE))
#> class: SpatialExperiment
#> dim: 50 99
#> metadata(0):
#> assays(1): counts
#> rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
#> ENSMUSG00000005886 ENSMUSG00000101476
#> rowData names(1): symbol
#> colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
#> AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1
#> colData names(4): in_tissue array_row array_col sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(4): sample_id image_id data scaleFactor
#>
#> rd10xV> # tabulate number of spots mapped to tissue
#> rd10xV> cd <- colData(spe)
#>
#> rd10xV> table(
#> rd10xV+ in_tissue = cd$in_tissue,
#> rd10xV+ sample_id = cd$sample_id)
#> sample_id
#> in_tissue section1 section2
#> FALSE 28 27
#> TRUE 22 22
#>
#> rd10xV> # view available images
#> rd10xV> imgData(spe)
#> DataFrame with 2 rows and 4 columns
#> sample_id image_id data scaleFactor
#> <character> <character> <list> <numeric>
#> 1 section1 lowres #### 0.0510334
#> 2 section2 lowres #### 0.0510334
# empty replacement retains sample identifiers
colData(spe) <- NULL
names(colData(spe))
#> [1] "sample_id"
# replacement of sample identifiers
# requires one-to-one mapping
## invalid replacement
tryCatch(
spe$sample_id <- seq(ncol(spe)),
error = function(e) message(e))
#> Error in .local(x, ..., value): Number of unique 'sample_id's is 2, but 99 were provided.
## valid replacement
old <- c("section1", "section2")
new <- c("sample_A", "sample_B")
idx <- match(spe$sample_id, old)
tmp <- spe
tmp$sample_id <- new[idx]
table(spe$sample_id, tmp$sample_id)
#>
#> sample_A sample_B
#> section1 50 0
#> section2 0 49