![[Superseded]](figures/lifecycle-superseded.svg)
sample_n() and sample_frac() have been superseded in favour of
slice_sample(). While they will not be deprecated in the near future,
retirement means that we will only perform critical bug fixes, so we recommend
moving to the newer alternative.
These functions were superseded because we realised it was more convenient to
have two mutually exclusive arguments to one function, rather than two
separate functions. This also made it to clean up a few other smaller
design issues with sample_n()/sample_frac:
The connection to
slice()was not obvious.The name of the first argument,
tbl, is inconsistent with other single table verbs which use.data.The
sizeargument uses tidy evaluation, which is surprising and undocumented.It was easier to remove the deprecated
.envargument....was in a suboptimal position.
# S3 method for class 'SpatialExperiment'
sample_n(tbl, size, replace = FALSE, weight = NULL, .env = NULL, ...)
# S3 method for class 'SpatialExperiment'
sample_frac(tbl, size = 1, replace = FALSE, weight = NULL, .env = NULL, ...)Arguments
- tbl
A data.frame.
- size
<
tidy-select> Forsample_n(), the number of rows to select. Forsample_frac(), the fraction of rows to select. Iftblis grouped,sizeapplies to each group.- replace
Sample with or without replacement?
- weight
<
tidy-select> Sampling weights. This must evaluate to a vector of non-negative numbers the same length as the input. Weights are automatically standardised to sum to 1.- .env
DEPRECATED.
- ...
ignored
Value
tidySpatialExperiment
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] "/home/runner/work/_temp/Library/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))
#> # A SpatialExperiment-tibble abstraction: 99 × 7
#> # Features = 50 | Cells = 99 | Assays = counts
#> .cell in_tissue array_row array_col sample_id pxl_col_in_fullres
#> <chr> <lgl> <int> <int> <chr> <int>
#> 1 AAACAACGAATAGTTC-1 FALSE 0 16 section1 2312
#> 2 AAACAAGTATCTCCCA-1 TRUE 50 102 section1 8230
#> 3 AAACAATCTACTAGCA-1 TRUE 3 43 section1 4170
#> 4 AAACACCAATAACTGC-1 TRUE 59 19 section1 2519
#> 5 AAACAGAGCGACTCCT-1 TRUE 14 94 section1 7679
#> 6 AAACAGCTTTCAGAAG-1 FALSE 43 9 section1 1831
#> 7 AAACAGGGTCTATATT-1 FALSE 47 13 section1 2106
#> 8 AAACAGTGTTCCTGGG-1 FALSE 73 43 section1 4170
#> 9 AAACATGGTGAGAGGA-1 FALSE 62 0 section1 1212
#> 10 AAACATTTCCCGGATT-1 FALSE 61 97 section1 7886
#> # ℹ 89 more rows
#> # ℹ 1 more variable: pxl_row_in_fullres <int>
#>
#> 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))
#> # A SpatialExperiment-tibble abstraction: 99 × 7
#> # Features = 50 | Cells = 99 | Assays = counts
#> .cell in_tissue array_row array_col sample_id pxl_col_in_fullres
#> <chr> <lgl> <int> <int> <chr> <int>
#> 1 AAACAACGAATAGTTC-1 FALSE 0 16 section1 2312
#> 2 AAACAAGTATCTCCCA-1 TRUE 50 102 section1 8230
#> 3 AAACAATCTACTAGCA-1 TRUE 3 43 section1 4170
#> 4 AAACACCAATAACTGC-1 TRUE 59 19 section1 2519
#> 5 AAACAGAGCGACTCCT-1 TRUE 14 94 section1 7679
#> 6 AAACAGCTTTCAGAAG-1 FALSE 43 9 section1 1831
#> 7 AAACAGGGTCTATATT-1 FALSE 47 13 section1 2106
#> 8 AAACAGTGTTCCTGGG-1 FALSE 73 43 section1 4170
#> 9 AAACATGGTGAGAGGA-1 FALSE 62 0 section1 1212
#> 10 AAACATTTCCCGGATT-1 FALSE 61 97 section1 7886
#> # ℹ 89 more rows
#> # ℹ 1 more variable: pxl_row_in_fullres <int>
#>
#> 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
spe |>
sample_n(10)
#> # A SpatialExperiment-tibble abstraction: 10 × 7
#> # Features = 50 | Cells = 10 | Assays = counts
#> .cell in_tissue array_row array_col sample_id pxl_col_in_fullres
#> <chr> <lgl> <int> <int> <chr> <int>
#> 1 AAACCTAAGCAGCCGG-1 FALSE 65 83 section1 6922
#> 2 AAACGGGTTGGTATCC-1 FALSE 1 23 section1 2794
#> 3 AAAGACCCAAGTCGCG-1 TRUE 10 48 section1 4514
#> 4 AAACAGTGTTCCTGGG-1 FALSE 73 43 section1 4170
#> 5 AAACTTGCAAACGTAT-1 TRUE 45 19 section1 2519
#> 6 AAAGAATGACCTTAGA-1 FALSE 64 2 section1 1349
#> 7 AAAGGGATGTAGCAAG-1 TRUE 24 62 section1 5477
#> 8 AAACTAACGTGGCGAC-1 FALSE 8 110 section1 8780
#> 9 AAAGTCACTGATGTAA-1 TRUE 10 52 section1 4789
#> 10 AAACGGTTGCGAACTG-1 TRUE 67 59 section1 5271
#> # ℹ 1 more variable: pxl_row_in_fullres <int>
spe |>
sample_frac(0.1)
#> tidySpatialExperiment says: When sampling with replacement a data frame is returned
#> for independent data analysis.
#> # A tibble: 20 × 7
#> .cell in_tissue array_row array_col sample_id pxl_col_in_fullres
#> <chr> <lgl> <int> <int> <chr> <int>
#> 1 AAACAAGTATCTCCCA-1 TRUE 50 102 section1 8230
#> 2 AAACAATCTACTAGCA-1 TRUE 3 43 section1 4170
#> 3 AAACAGCTTTCAGAAG-1 FALSE 43 9 section1 1831
#> 4 AAACCTAAGCAGCCGG-1 FALSE 65 83 section1 6922
#> 5 AAACGAAGATGGAGTA-1 FALSE 58 4 section1 1487
#> 6 AAACGCCCGAGATCGG-1 FALSE 4 108 section1 8642
#> 7 AAAGAATGTGGACTAA-1 FALSE 71 105 section1 8436
#> 8 AAAGACTGGGCGCTTT-1 FALSE 29 15 section1 2243
#> 9 AAAGACTGGGCGCTTT-1 FALSE 29 15 section1 2243
#> 10 AAAGGCTACGGACCAT-1 TRUE 62 54 section1 4927
#> 11 AAACAAGTATCTCCCA-1 TRUE 50 102 section2 8230
#> 12 AAACAATCTACTAGCA-1 TRUE 3 43 section2 4170
#> 13 AAACAGCTTTCAGAAG-1 FALSE 43 9 section2 1831
#> 14 AAACCTAAGCAGCCGG-1 FALSE 65 83 section2 6922
#> 15 AAACGAAGATGGAGTA-1 FALSE 58 4 section2 1487
#> 16 AAACGCCCGAGATCGG-1 FALSE 4 108 section2 8642
#> 17 AAAGAATGTGGACTAA-1 FALSE 71 105 section2 8436
#> 18 AAAGACTGGGCGCTTT-1 FALSE 29 15 section2 2243
#> 19 AAAGACTGGGCGCTTT-1 FALSE 29 15 section2 2243
#> 20 AAAGGCTACGGACCAT-1 TRUE 62 54 section2 4927
#> # ℹ 1 more variable: pxl_row_in_fullres <int>