tests/testthat/test-do_DimPlot.R

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

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

  testthat::test_that("do_DimPlot: CRAN essentials", {
    p <- SCpubr::do_DimPlot(sample = sample)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample, idents.highlight = "0")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample, split.by = "seurat_clusters")
    testthat::expect_type(p, "list")

    sample$orig.ident <- sample(c("A", "B"), ncol(sample), replace = TRUE)
    p <- SCpubr::do_DimPlot(sample = sample, group.by = "seurat_clusters", split.by = "orig.ident")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - sample", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - contour", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            plot_density_contour = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            plot_density_contour = TRUE,
                            contour.position = "bottom")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            plot_density_contour = TRUE,
                            contour.position = "top")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation",
                            raster = TRUE,
                            plot_density_contour = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation",
                            raster = TRUE,
                            plot_density_contour = TRUE,
                            contour.position = "top")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation",
                            raster = TRUE,
                            label = TRUE,
                            plot_density_contour = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation",
                            raster = TRUE,
                            label = TRUE,
                            plot_density_contour = TRUE,
                            contour.position = "top")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            split.by = "annotation",
                            raster = TRUE,
                            plot_density_contour = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            split.by = "annotation",
                            raster = TRUE,
                            plot_density_contour = TRUE,
                            contour.position = "top")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            split.by = "annotation",
                            raster = TRUE,
                            label = TRUE,
                            plot_density_contour = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            split.by = "annotation",
                            raster = TRUE,
                            label = TRUE,
                            plot_density_contour = TRUE,
                            contour.position = "top")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            idents.highlight = "0",
                            raster = TRUE,
                            plot_density_contour = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            idents.highlight = "0",
                            raster = TRUE,
                            plot_density_contour = TRUE,
                            contour.position = "top")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            idents.highlight = "0",
                            raster = TRUE,
                            label = TRUE,
                            plot_density_contour = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            idents.highlight = "0",
                            raster = TRUE,
                            label = TRUE,
                            plot_density_contour = TRUE,
                            contour.position = "top")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - group.by + split.by", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation",
                            label = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation",
                            raster = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation",
                            raster = TRUE,
                            label = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            split.by = "annotation",
                            raster = TRUE,
                            label = TRUE)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - plot axis", {
    testthat::skip_on_cran()



    p <- SCpubr::do_DimPlot(sample = sample, plot.axes = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample, reduction = "pca", plot.axes = TRUE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample, dims = c(2, 1), plot.axes = TRUE)
    testthat::expect_type(p, "list")

    sample@reductions$diffusion <- sample@reductions$umap
    p <- SCpubr::do_DimPlot(sample = sample,
                            reduction = "diffusion",
                            plot.axes = TRUE)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - sample cell_borders", {
    testthat::skip_on_cran()



    p <- SCpubr::do_DimPlot(sample = sample, plot_cell_borders = TRUE)
    testthat::expect_type(p, "list")
    p <- SCpubr::do_DimPlot(sample = sample, plot_cell_borders = TRUE, raster = TRUE, pt.size = 1)
    testthat::expect_type(p, "list")
    p <- SCpubr::do_DimPlot(sample = sample, plot_cell_borders = TRUE, idents.highlight = "1")
    testthat::expect_type(p, "list")
    p <- SCpubr::do_DimPlot(sample = sample, plot_cell_borders = TRUE, raster = TRUE, idents.highlight = "1", pt.size = 1)
    testthat::expect_type(p, "list")
    p <- SCpubr::do_DimPlot(sample = sample, plot_cell_borders = TRUE, split.by = "seurat_clusters")
    testthat::expect_type(p, "list")
    p <- SCpubr::do_DimPlot(sample = sample, plot_cell_borders = TRUE, raster = TRUE, split.by = "seurat_clusters", pt.size = 1)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - sample marginal", {

    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            plot_marginal_distributions = TRUE,
                            marginal.type = "density",
                            plot_cell_borders = FALSE)
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            plot_marginal_distributions = TRUE,
                            marginal.type = "histogram",
                            plot_cell_borders = FALSE)
    testthat::expect_type(p, "list")

    p <- suppressWarnings({SCpubr::do_DimPlot(sample = sample,
                                              plot_marginal_distributions = TRUE,
                                              plot_cell_borders = FALSE,
                                              marginal.type = "violin")})
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample,
                            plot_marginal_distributions = TRUE,
                            marginal.type = "boxplot",
                            plot_cell_borders = FALSE)
    testthat::expect_type(p, "list")

    #p <- SCpubr::do_DimPlot(sample = sample,
    #                        plot_marginal_distributions = TRUE,
    #                        marginal.type = "densigram",
    #                        plot_cell_borders = FALSE)
    #testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - sample marginal size", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            plot_marginal_distributions = TRUE,
                            marginal.size = 9,
                            plot_cell_borders = FALSE)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - sample marginal group", {

    testthat::skip_on_cran()

    p <- SCpubr::do_DimPlot(sample = sample,
                            plot_marginal_distributions = TRUE,
                            marginal.group = FALSE,
                            plot_cell_borders = FALSE)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: FAIL - sample marginal wrong marginal.type", {
    testthat::skip_on_cran()


    testthat::expect_error({SCpubr::do_DimPlot(sample = sample,
                                               plot_marginal_distributions = TRUE,
                                               plot_cell_borders = FALSE,
                                               marginal.type = "wrong")})
  })

  testthat::test_that("do_DimPlot: FAIL - sample marginal used alongside split.by or cells.highlight", {
    testthat::skip_on_cran()


    testthat::expect_error({SCpubr::do_DimPlot(sample = sample,
                                               plot_marginal_distributions = TRUE,
                                               plot_cell_borders = FALSE,
                                               split.by = "seurat_clusters")})

    testthat::expect_error({SCpubr::do_DimPlot(sample = sample,
                                               plot_marginal_distributions = TRUE,
                                               plot_cell_borders = FALSE,
                                               cells.highlight =  colnames(sample))})

    testthat::expect_error({SCpubr::do_DimPlot(sample = sample,
                                               plot_marginal_distributions = TRUE,
                                               plot_cell_borders = FALSE,
                                               idents.highlight =  "1")})
  })

  testthat::test_that("do_DimPlot: PASS - title", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            plot.title = "My awesome SC data set")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - subtitle", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            plot.subtitle = "My awesome SC data set")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - caption", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            plot.caption = "My awesome SC data set")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - sample + group.by", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, group.by = "seurat_clusters")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - sample + split.by", {

    testthat::skip_on_cran()

    p <- SCpubr::do_DimPlot(sample = sample, split.by = "seurat_clusters")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - sample + split.by + idents.keep", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, split.by = "seurat_clusters", idents.keep = c("1", "3", "5"))
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample, split.by = "seurat_clusters", group.by = "annotation", idents.keep = c("1", "3", "5"))
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - dims", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, dims = c(1, 2))
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - legend.position", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, legend.position = "top")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - legend.ncol", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, legend.ncol = 2)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - legend.nrow", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, legend.nrow = 2)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - label", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, label = TRUE)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - order", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, order = "5", shuffle = FALSE)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - colors.use", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, colors.use = c("0" = "#001219",
                                                            "1" = "#005f73",
                                                            "2" = "#0a9396",
                                                            "3" = "#94d2bd",
                                                            "4" = "#e9d8a6",
                                                            "5" = "#ee9b00",
                                                            "6" = "#ca6702",
                                                            "7" = "#bb3e03",
                                                            "8" = "#ae2012"))

    p <- SCpubr::do_DimPlot(sample = sample, colors.use = c("Cell" = "#001219"),
                            split.by = "orig.ident")
    testthat::expect_type(p, "list")

    p <- SCpubr::do_DimPlot(sample = sample, colors.use = c("Cell" = "#001219"),
                            group.by = "orig.ident",
                            split.by = "seurat_clusters")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - cells.highlight", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, cells.highlight = sample(colnames(sample), 50))
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - idents.highlight", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, idents.highlight = "5")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - cells.highlight and idents.highlight", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, cells.highlight = sample(colnames(sample), 50), idents.highlight = "2")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - idents.keep", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, idents.keep = "5")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: FAIL - group.by and cells.highlights used", {
    testthat::skip_on_cran()


    testthat::expect_error(SCpubr::do_DimPlot(sample = sample, group.by = "seurat_clusters", cells.highlight = colnames(sample)))
  })

  testthat::test_that("do_DimPlot: FAIL - split.by and cells.highlights used", {
    testthat::skip_on_cran()


    testthat::expect_error(SCpubr::do_DimPlot(sample = sample, split.by = "seurat_clusters", cells.highlight = colnames(sample)))
  })

  testthat::test_that("do_DimPlot: WARNING - order and shuffle used", {
    testthat::skip_on_cran()


    testthat::expect_warning(SCpubr::do_DimPlot(sample = sample, order = "4", shuffle = TRUE))
  })

  testthat::test_that("do_DimPlot: FAIL - more than one NA values", {
    testthat::skip_on_cran()


    testthat::expect_error(SCpubr::do_DimPlot(sample = sample, na.value = c("red", "blue")))
  })

  testthat::test_that("do_DimPlot: WARNING - raster = TRUE and pt.size lower than 1", {
    testthat::skip_on_cran()


    testthat::expect_warning(SCpubr::do_DimPlot(sample = sample, raster = TRUE, pt.size = 0.5))
  })

  colors <- c("0" = "#001219",
              "1" = "#005f73",
              "2" = "#0a9396",
              "3" = "#94d2bd",
              "4" = "#e9d8a6",
              "5" = "#ee9b00",
              "6" = "#ca6702",
              "7" = "#bb3e03",
              "8" = "#ae2012")

  testthat::test_that("do_DimPlot: PASS - group.by + colors", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, group.by = "seurat_clusters", colors.use = colors)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - split.by + colors", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, split.by = "seurat_clusters", colors.use = colors)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: FAIL - more than 1 color with cells highlight", {
    testthat::skip_on_cran()


    testthat::expect_error(SCpubr::do_DimPlot(sample = sample, colors.use = colors, idents.highlight = "4"))
  })

  testthat::test_that("do_DimPlot: FAIL - idents.keep not in the levels of the sample", {
    testthat::skip_on_cran()


    testthat::expect_error(SCpubr::do_DimPlot(sample = sample, idents.keep = c("4", "Not an ident")))
  })

  testthat::test_that("do_DimPlot: FAIL - idents.keep not in the unique values of group.by", {
    testthat::skip_on_cran()


    testthat::expect_error(SCpubr::do_DimPlot(sample = sample, group.by = "orig.ident", idents.keep = c("4", "Not an ident")))
  })

  testthat::test_that("do_DimPlot: FAIL - idents.keep not in the unique values of split.by", {
    testthat::skip_on_cran()


    testthat::expect_error(SCpubr::do_DimPlot(sample = sample, split.by = "orig.ident", idents.keep = c("4", "Not an ident")))
  })


  testthat::test_that("do_DimPlot: PASS - split.by + plot.title, subtitle and caption", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample, split.by = "orig.ident",
                            plot.title = "Plot title",
                            plot.subtitle = "Plot subtitle",
                            plot.caption = "Plot caption")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - legend.position none", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            legend.position = "none")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - dims different", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            dims = c(2, 1))
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - diffusion maps", {
    testthat::skip_on_cran()


    sample@reductions$diffusion <- sample@reductions$umap
    p <- SCpubr::do_DimPlot(sample = sample,
                            reduction = "diffusion")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - group.by + idents.keep", {
    testthat::skip_on_cran()


    p <- SCpubr::do_DimPlot(sample = sample,
                            group.by = "seurat_clusters",
                            idents.keep = "4")
    testthat::expect_type(p, "list")
  })


  testthat::test_that("do_DimPlot: PASS - split.by + factor", {
    testthat::skip_on_cran()


    sample$seurat_clusters <- factor(sample$seurat_clusters)
    p <- SCpubr::do_DimPlot(sample = sample, split.by = "seurat_clusters", colors.use = colors)
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: PASS - split.by + factor + idents.keep", {
    testthat::skip_on_cran()


    sample$seurat_clusters <- factor(sample$seurat_clusters)
    p <- SCpubr::do_DimPlot(sample = sample, split.by = "seurat_clusters", colors.use = colors, idents.keep = "4")
    testthat::expect_type(p, "list")
  })

  testthat::test_that("do_DimPlot: FAIL - wrong font.type", {
    testthat::skip_on_cran()


    testthat::expect_error(SCpubr::do_DimPlot(sample = sample, font.type = "wrong"))
  })
}