tests/testthat/test-do_RidgePlot.R

In enblacar/SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

if(base::isFALSE(dep_check[["do_RidgePlot"]])){

  testthat::test_that("do_RidgePlot: CRAN essentials", {

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              use_viridis = TRUE,
                              viridis.direction = 1)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              compute_distribution_tails = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              compute_distribution_tails = TRUE,
                              prob_tails = 0.4)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              color_by_probabilities = TRUE)
    testthat::expect_type(p, "list")

  })

  testthat::test_that("do_RidgePlot: PASS - default", {
    testthat::skip_on_cran()

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              use_viridis = TRUE,
                              viridis.direction = 1)
    testthat::expect_type(p, "list")
    
    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              use_viridis = TRUE,
                              viridis.direction = -1)
    testthat::expect_type(p, "list")
    
    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              use_viridis = FALSE,
                              sequential.direction = 1)
    testthat::expect_type(p, "list")
    
    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              use_viridis = FALSE,
                              sequential.direction = -1)
    testthat::expect_type(p, "list")
    
    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              color_by_probabilities = TRUE,
                              use_viridis = TRUE,
                              viridis.direction = 1)
    testthat::expect_type(p, "list")
    
    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              color_by_probabilities = TRUE,
                              use_viridis = TRUE,
                              viridis.direction = -1)
    testthat::expect_type(p, "list")
    
    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              color_by_probabilities = TRUE,
                              use_viridis = FALSE,
                              sequential.direction = 1)
    testthat::expect_type(p, "list")
    
    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              color_by_probabilities = TRUE,
                              use_viridis = FALSE,
                              sequential.direction = -1)
    testthat::expect_type(p, "list")
    
    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              group.by = "orig.ident")
    testthat::expect_type(p, "list")

    sample$orig.ident <- factor(sample$orig.ident)

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              group.by = "orig.ident")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              legend.position = "bottom")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              group.by = "orig.ident",
                              legend.position = "bottom",
                              colors.use = c("Cell" = "red"))
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_RidgePlot: PASS - plot.grid", {
    testthat::skip_on_cran()


    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              plot.grid = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              plot.grid = FALSE)
    testthat::expect_type(p, "list")
  })


  testthat::test_that("do_RidgePlot: PASS - split.by", {
    testthat::skip_on_cran()


    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              split.by = "orig.ident")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_RidgePlot: PASS - continuous scale", {
    testthat::skip_on_cran()


    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              viridis.direction = 1)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              viridis.direction = -1)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_RidgePlot: PASS - group.by", {
    testthat::skip_on_cran()


    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              group.by = "orig.ident")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_RidgePlot: PASS - quantiles", {
    testthat::skip_on_cran()


    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              compute_custom_quantiles = TRUE,
                              compute_quantiles = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              compute_custom_quantiles = TRUE,
                              compute_quantiles = TRUE,
                              quantiles = c(0.1, 0.5, 0.9))
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_RidgePlot: PASS - distribution tails", {
    testthat::skip_on_cran()


    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              compute_distribution_tails = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nCount_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              compute_distribution_tails = TRUE,
                              prob_tails = 0.4)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_RidgePlot: PASS - distribution tails", {
    testthat::skip_on_cran()


    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              continuous_scale = TRUE,
                              compute_quantiles = TRUE,
                              color_by_probabilities = TRUE)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_RidgePlot: PASS - flip", {
    testthat::skip_on_cran()


    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              flip = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_RidgePlot(sample = sample,
                              feature = "nFeature_RNA",
                              flip = FALSE)
    testthat::expect_type(p, "list")
  })
}