The subsetting method for SpatialExperiment objects ensures
that spatial data attributes (spatialCoords and
imgData) are subsetted correctly to match rows and columns with
the remainder of the object.
Arguments
- x
a
SpatialExperimentobject- i
row indices for subsetting
- j
column indices for subsetting
Value
a SpatialExperiment object
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
dim(spe)
#> [1] 50 99
set.seed(123)
idx <- sample(ncol(spe), 10)
sub <- spe[, idx]
dim(sub)
#> [1] 50 10
colData(sub)
#> DataFrame with 10 rows and 4 columns
#> in_tissue array_row array_col sample_id
#> <logical> <integer> <integer> <character>
#> AAACTGCTGGCTCCAA-1 TRUE 45 67 section1
#> AAACTCGTGATATAAG-1 FALSE 23 113 section2
#> AAACAAGTATCTCCCA-1 TRUE 50 102 section2
#> AAACCGGGTAGGTACC-1 TRUE 42 28 section1
#> AAACGAAGAACATACC-1 TRUE 6 64 section2
#> AAAGGCTCTCGCGCCG-1 TRUE 55 55 section1
#> AAAGTGCCATCAATTA-1 FALSE 63 125 section1
#> AAAGGGATGTAGCAAG-1 TRUE 24 62 section1
#> AAAGTAGCATTGCTCA-1 TRUE 51 27 section2
#> AAACGGGTTGGTATCC-1 FALSE 1 23 section1
spatialCoords(sub)
#> pxl_col_in_fullres pxl_row_in_fullres
#> AAACTGCTGGCTCCAA-1 5821 6639
#> AAACTCGTGATATAAG-1 8986 4005
#> AAACAAGTATCTCCCA-1 8230 7237
#> AAACCGGGTAGGTACC-1 3138 6280
#> AAACGAAGAACATACC-1 5615 1970
#> AAAGGCTCTCGCGCCG-1 4996 7836
#> AAAGTGCCATCAATTA-1 9812 8793
#> AAAGGGATGTAGCAAG-1 5477 4125
#> AAAGTAGCATTGCTCA-1 3069 7357
#> AAACGGGTTGGTATCC-1 2794 1371