tests/testthat/test-dplyr_methods.R

In stemangiola/tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse

context("dplyr test")

library(tidySummarizedExperiment)


test_that("bind_rows", {
    pasilla_bind <- bind_rows(pasilla, pasilla)

    pasilla_bind %>%
        count(.sample, .feature) %>%
        dplyr::count(n) %>%
        filter(n > 1) %>%
        nrow() %>%
        expect_equal(0)
})

test_that("distinct", {
    pasilla %>%
        distinct(condition) %>%
        ncol() %>%
        expect_equal(1)
})

test_that("filter", {
    pasilla %>%
        filter(condition == "untreated") %>%
        nrow() %>%
        expect_equal(14599)
})

test_that("group_by", {
    pasilla %>%
        group_by(condition) %>%
        ncol() %>%
        expect_equal(5)
})

test_that("summarise", {
    pasilla %>%
        summarise(mean(counts)) %>%
        nrow() %>%
        expect_equal(1)
})

test_that("mutate", {
    pasilla %>%
        mutate(condition = 1) %>%
        distinct(condition) %>%
        nrow() %>%
        expect_equal(1)
})

test_that("rename", {
    pasilla %>%
        rename(groups = condition) %>%
        select(groups) %>%
        ncol() %>%
        expect_equal(1)
})

test_that("left_join", {
    expect_equal(
        pasilla %>%
            left_join(pasilla %>%
                          distinct(condition) %>%
                          mutate(new_column = 1:2)) %>%
            colData() %>%
            ncol(),
        pasilla %>%
            colData() %>%
            ncol() %>%
            sum(1)
    )
})

test_that("left_join 0 samples", {
 
    pasilla[0,] %>%
      left_join(pasilla %>%
                  distinct(condition) %>%
                  mutate(new_column = 1)) |> 
    as_tibble() |> 
      pull(new_column) %>%
      unique() |> 
      expect_equal(1)
  
})

test_that("inner_join", {
    pasilla %>% inner_join(pasilla %>%
                          distinct(condition) %>%
                          mutate(new_column = 1:2) %>%
                          slice(1)) %>%
        ncol() %>%
        expect_equal(4)
})

test_that("right_join", {
    pasilla %>% right_join(pasilla %>%
                          distinct(condition) %>%
                          mutate(new_column = 1:2) %>%
                          slice(1)) %>%
        ncol() %>%
        expect_equal(4)
})

test_that("full_join", {
    pasilla %>%
        full_join(tibble::tibble(condition = "A",     other = 1:4)) %>% nrow() %>%
        expect_equal(102197)
})

test_that("slice", {
    pasilla %>%
        slice(1) %>%
        ncol() %>%
        expect_equal(1)
})

test_that("select", {
    pasilla %>%
        select(-condition) %>%
        class() %>%
        as.character() %>%
        expect_equal("SummarizedExperiment")

    pasilla %>%
        select(condition) %>%
        class() %>%
        as.character() %>%
        .[1] %>%
        expect_equal("tbl_df")
})

test_that("sample_n", {
    pasilla %>%
        sample_n(50) %>%
        nrow() %>%
        expect_equal(50)
})

test_that("sample_frac", {
    pasilla %>%
        sample_frac(0.1) %>%
        nrow() %>%
        expect_equal(10219)
})

test_that("count", {
    pasilla %>%
        count(condition) %>%
        nrow() %>%
        expect_equal(2)
})

test_that("mutate counts", {
  
  se = tidySummarizedExperiment::pasilla |> mutate(counts_2 = counts) 

  se |> 
    pull(counts) |> 
    expect_equal(
      se |> pull(counts_2)
    )
  
  se = tidySummarizedExperiment::pasilla 
  assays(se, withDimnames = FALSE)$counts_2 = assays(se)$counts[,7:1]
  
  se |> 
    pull(counts) |> 
    expect_equal(
      se |> pull(counts_2)
    )
  
  se |> 
  tidySummarizedExperiment:::check_if_assays_are_NOT_overlapped(dim = "cols") |> 
    expect_equal(FALSE)
  
  se[,1] |> 
    tidySummarizedExperiment:::check_if_assays_are_NOT_overlapped(dim = "cols") |> 
    expect_equal(TRUE)
  
  })

test_that("group_split splits character columns", {
  data(pasilla)
  pasilla |> 
    group_split(condition) |> 
    length() |> 
    expect_equal(2)
})

test_that("group_split splits logical comparisons", {
  data(pasilla)
  pasilla |> 
    group_split(counts > 0) |> 
    length() |> 
    expect_equal(2)
})

test_that("group_split splits with mutliple arguments", {
  data(pasilla)
  pasilla |> 
    group_split(condition, counts > 0) |> 
    length() |> 
    expect_equal(4)
})

test_that("mutate features", {
  pasilla %>%
    mutate_features(new = 1:nrow(pasilla)) %>%
    rowData() %>%
    as_tibble() %>%
    pull(new) %>%
    expect_equal(1:nrow(pasilla))
})

test_that("mutate samples", {
  pasilla %>%
    mutate_samples(new = 1:ncol(pasilla)) %>%
    colData() %>%
    as_tibble() %>%
    pull(new) %>%
    expect_equal(1:ncol(pasilla))
})