Unite multiple columns into one by pasting strings together

Convenience function to paste together multiple columns into one.

# S3 method for class 'SpatialExperiment'
unite(data, col, ..., sep = "_", remove = TRUE, na.rm = FALSE)

Arguments

data

A data frame.

col

The name of the new column, as a string or symbol.

This argument is passed by expression and supports quasiquotation (you can unquote strings and symbols). The name is captured from the expression with rlang::ensym() (note that this kind of interface where symbols do not represent actual objects is now discouraged in the tidyverse; we support it here for backward compatibility).

...

<tidy-select> Columns to unite

sep

Separator to use between values.

remove

If TRUE, remove input columns from output data frame.

na.rm

If TRUE, missing values will be removed prior to uniting each value.

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))
#> Warning: 'read10xVisium' is deprecated.
#> Use 'VisiumIO::TENxVisium(List)' instead.
#> See help("Deprecated")
#> # 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))
#> Warning: 'read10xVisium' is deprecated.
#> Use 'VisiumIO::TENxVisium(List)' instead.
#> See help("Deprecated")
#> # 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 |>
    unite("A", array_row:array_col)
#> # A SpatialExperiment-tibble abstraction: 99 × 6
#> # Features = 50 | Cells = 99 | Assays = counts
#>    .cell         in_tissue A     sample_id pxl_col_in_fullres pxl_row_in_fullres
#>    <chr>         <lgl>     <chr> <chr>                  <int>              <int>
#>  1 AAACAACGAATA… FALSE     0_16  section1                2312               1252
#>  2 AAACAAGTATCT… TRUE      50_1… section1                8230               7237
#>  3 AAACAATCTACT… TRUE      3_43  section1                4170               1611
#>  4 AAACACCAATAA… TRUE      59_19 section1                2519               8315
#>  5 AAACAGAGCGAC… TRUE      14_94 section1                7679               2927
#>  6 AAACAGCTTTCA… FALSE     43_9  section1                1831               6400
#>  7 AAACAGGGTCTA… FALSE     47_13 section1                2106               6879
#>  8 AAACAGTGTTCC… FALSE     73_43 section1                4170               9991
#>  9 AAACATGGTGAG… FALSE     62_0  section1                1212               8674
#> 10 AAACATTTCCCG… FALSE     61_97 section1                7886               8554
#> # ℹ 89 more rows

Unite multiple columns into one by pasting strings together

Arguments

Value

See also

Examples