arrange() orders either the rows or columns of a SummarizedExperiment
object. Note, to guarentee a valid SummarizedExperiment is returned,
arranging in the assays evaluation context is disabled.
Unlike other dplyr verbs, arrange() largely ignores grouping. The
SummarizedExperiment method also provides the same functionality via the
.by_group argument.
Usage
# S3 method for class 'SummarizedExperiment'
arrange(.data, ..., .by_group = FALSE)Arguments
- .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> Variables, or functions of variables. Usedesc()to sort a variable in descending order.- .by_group
If
TRUE, will sort first by grouping variable. Applies to grouped data frames only.
Examples
#arrange within rows/cols contexts separately
arrange(se_simple,
rows(direction),
cols(dplyr::desc(condition)))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | counts logcounts | gene length direction | sample
#> <chr> <chr> | <int> <dbl> | <chr> <int> <chr> | <chr>
#> 1 row_2 col_3 | 1 0 | g2 24 + | s3
#> 2 row_3 col_3 | 15 2.71 | g3 60 + | s3
#> 3 row_5 col_3 | 12 2.48 | g5 37 + | s3
#> 4 row_1 col_3 | 7 1.95 | g1 1 - | s3
#> 5 row_4 col_3 | 10 2.30 | g4 39 - | s3
#> … … … … … … … … …
#> n-4 row_2 col_2 | 2 0.693 | g2 24 + | s2
#> n-3 row_3 col_2 | 6 1.79 | g3 60 + | s2
#> n-2 row_5 col_2 | 13 2.56 | g5 37 + | s2
#> n-1 row_1 col_2 | 8 2.08 | g1 1 - | s2
#> n row_4 col_2 | 17 2.83 | g4 39 - | s2
#> # ℹ n = 20
#> # ℹ 1 more variable: condition <chr>
# access assay data to compute arrangement
arrange(se_simple,
rows(rowSums(.assays_asis$counts)),
cols(colSums(.assays_asis$counts)))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | counts logcounts | gene length direction | sample
#> <chr> <chr> | <int> <dbl> | <chr> <int> <chr> | <chr>
#> 1 row_2 col_4 | 4 1.39 | g2 24 + | s4
#> 2 row_1 col_4 | 9 2.20 | g1 1 - | s4
#> 3 row_4 col_4 | 3 1.10 | g4 39 - | s4
#> 4 row_5 col_4 | 5 1.61 | g5 37 + | s4
#> 5 row_3 col_4 | 20 3.00 | g3 60 + | s4
#> … … … … … … … … …
#> n-4 row_2 col_1 | 19 2.94 | g2 24 + | s1
#> n-3 row_1 col_1 | 14 2.64 | g1 1 - | s1
#> n-2 row_4 col_1 | 11 2.40 | g4 39 - | s1
#> n-1 row_5 col_1 | 18 2.89 | g5 37 + | s1
#> n row_3 col_1 | 16 2.77 | g3 60 + | s1
#> # ℹ n = 20
#> # ℹ 1 more variable: condition <chr>
# assay context is disabled
arrange(se_simple, counts) |> try()
#> Error in arrange(se_simple, counts) : Cannot arrange in `assays` context
#> ✖ review expression indices 1 in dots
#> ℹ consider wrapping expressions in rows(...) or cols(...)
# convert to `data.frame` first
as.data.frame(se_simple) |>
arrange(counts)
#> .features .samples counts logcounts gene length direction sample condition
#> 1 row_2 col_3 1 0.0000000 g2 24 + s3 drug
#> 2 row_2 col_2 2 0.6931472 g2 24 + s2 cntrl
#> 3 row_4 col_4 3 1.0986123 g4 39 - s4 drug
#> 4 row_2 col_4 4 1.3862944 g2 24 + s4 drug
#> 5 row_5 col_4 5 1.6094379 g5 37 + s4 drug
#> 6 row_3 col_2 6 1.7917595 g3 60 + s2 cntrl
#> 7 row_1 col_3 7 1.9459101 g1 1 - s3 drug
#> 8 row_1 col_2 8 2.0794415 g1 1 - s2 cntrl
#> 9 row_1 col_4 9 2.1972246 g1 1 - s4 drug
#> 10 row_4 col_3 10 2.3025851 g4 39 - s3 drug
#> 11 row_4 col_1 11 2.3978953 g4 39 - s1 cntrl
#> 12 row_5 col_3 12 2.4849066 g5 37 + s3 drug
#> 13 row_5 col_2 13 2.5649494 g5 37 + s2 cntrl
#> 14 row_1 col_1 14 2.6390573 g1 1 - s1 cntrl
#> 15 row_3 col_3 15 2.7080502 g3 60 + s3 drug
#> 16 row_3 col_1 16 2.7725887 g3 60 + s1 cntrl
#> 17 row_4 col_2 17 2.8332133 g4 39 - s2 cntrl
#> 18 row_5 col_1 18 2.8903718 g5 37 + s1 cntrl
#> 19 row_2 col_1 19 2.9444390 g2 24 + s1 cntrl
#> 20 row_3 col_4 20 2.9957323 g3 60 + s4 drug