mutate() creates new columns that are functions of existing variables.
It can also modify (if the name is the same as an existing
column) and delete columns (by setting their value to NULL).
# S3 method for SpatialExperiment
mutate(.data, ...)A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details.
<data-masking> Name-value pairs.
The name gives the name of the column in the output.
The value can be:
A vector of length 1, which will be recycled to the correct length.
A vector the same length as the current group (or the whole data frame if ungrouped).
NULL, to remove the column.
A data frame or tibble, to create multiple columns in the output.
An object of the same type as .data. The output has the following
properties:
Columns from .data will be preserved according to the .keep argument.
Existing columns that are modified by ... will always be returned in
their original location.
New columns created through ... will be placed according to the
.before and .after arguments.
The number of rows is not affected.
Columns given the value NULL will be removed.
Groups will be recomputed if a grouping variable is mutated.
Data frame attributes are preserved.
Because mutating expressions are computed within groups, they may yield different results on grouped tibbles. This will be the case as soon as an aggregating, lagging, or ranking function is involved. Compare this ungrouped mutate:
With the grouped equivalent:
starwars %>%
select(name, mass, species) %>%
group_by(species) %>%
mutate(mass_norm = mass / mean(mass, na.rm = TRUE))The former normalises mass by the global average whereas the
latter normalises by the averages within species levels.
This function is a generic, 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:
dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment), tidySpatialExperiment (SpatialExperiment)
.
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 |>
mutate(array_col = 1)
#> # 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> <dbl> <chr> <int>
#> 1 AAACAACGAATAGTTC-1 FALSE 0 1 section1 2312
#> 2 AAACAAGTATCTCCCA-1 TRUE 50 1 section1 8230
#> 3 AAACAATCTACTAGCA-1 TRUE 3 1 section1 4170
#> 4 AAACACCAATAACTGC-1 TRUE 59 1 section1 2519
#> 5 AAACAGAGCGACTCCT-1 TRUE 14 1 section1 7679
#> 6 AAACAGCTTTCAGAAG-1 FALSE 43 1 section1 1831
#> 7 AAACAGGGTCTATATT-1 FALSE 47 1 section1 2106
#> 8 AAACAGTGTTCCTGGG-1 FALSE 73 1 section1 4170
#> 9 AAACATGGTGAGAGGA-1 FALSE 62 1 section1 1212
#> 10 AAACATTTCCCGGATT-1 FALSE 61 1 section1 7886
#> # ℹ 89 more rows
#> # ℹ 1 more variable: pxl_row_in_fullres <int>