Subset rows using their positions

Source: R/dplyr_methods.R

slice() lets you index rows by their (integer) locations. It allows you to select, remove, and duplicate rows. It is accompanied by a number of helpers for common use cases:

  • slice_head() and slice_tail() select the first or last rows.

  • slice_sample() randomly selects rows.

  • slice_min() and slice_max() select rows with the smallest or largest values of a variable.

If .data is a grouped_df, the operation will be performed on each group, so that (e.g.) slice_head(df, n = 5) will select the first five rows in each group.

Value

An object of the same type as .data. The output has the following properties:

  • Each row may appear 0, 1, or many times in the output.

  • Columns are not modified.

  • Groups are not modified.

  • Data frame attributes are preserved.

Details

Slice does not work with relational databases because they have no intrinsic notion of row order. If you want to perform the equivalent operation, use filter() and row_number().

Methods

These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

Methods available in currently loaded packages:

  • slice(): (ANY, integer, numeric, Rle, RleList, XDouble, XInteger), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) .

  • slice_head(): dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

  • slice_tail(): dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

  • slice_min(): dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

  • slice_max(): dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

  • slice_sample(): dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

See also

Other single table verbs: arrange(), mutate(), rename(), summarise()

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] "/__w/_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 |>
   slice(1)
#> # A SpatialExperiment-tibble abstraction: 1 × 7
#> # Features = 50 | Cells = 1 | 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
#> # ℹ 1 more variable: pxl_row_in_fullres <int>