if (base::isFALSE(dep_check[["do_BeeSwarmPlot"]])){ testthat::test_that("do_BeeSwarmPlot: CRAN essentials", { p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - categorical variable dimred component", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = FALSE, legend.title = NULL) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = FALSE, legend.title = "A") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - cell_borders", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", plot_cell_borders = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", plot_cell_borders = TRUE, raster = TRUE, pt.size = 1) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - categorical variable gene", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, remove_x_axis = TRUE, remove_y_axis = TRUE, flip = TRUE, raster = TRUE, ylab = "Ylab") testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, remove_x_axis = TRUE, remove_y_axis = TRUE, flip = TRUE, raster = TRUE, ylab = NULL) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, order = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, raster = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, flip = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, flip = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "orig.ident", continuous_feature = FALSE, colors.use = c("Cell" = "red")) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, legend.title = NULL) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, order = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = TRUE, use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = TRUE, order = TRUE, use_viridis = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - legend position = right", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "EPC1", group.by = "seurat_clusters", continuous_feature = FALSE, legend.position = "right") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - categorical variable metadata", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "nCount_RNA", group.by = "seurat_clusters", continuous_feature = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - continuous variable", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - continuous variable legend normal", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE, legend.type = "normal") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - continuous variable legend colorbar", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE, legend.type = "colorbar") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: FAIL - wrong legend type", { testthat::skip_on_cran() testthat::expect_error(SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE, legend.type = "wrong")) }) testthat::test_that("do_BeeSwarmPlot: FAIL - more than one feature", { testthat::skip_on_cran() testthat::expect_error(SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = c("PC_1", "PC_2"), group.by = "seurat_clusters", continuous_feature = TRUE)) }) testthat::test_that("do_BeeSwarmPlot: FAIL - wrong legend position", { testthat::skip_on_cran() testthat::expect_error(SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE, legend.position = "wrong")) }) testthat::test_that("do_BeeSwarmPlot: FAIL - wrong font.type", { testthat::skip_on_cran() testthat::expect_error(SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE, font.type = "wrong")) }) testthat::test_that("do_BeeSwarmPlot: PASS - continuous variable viridis scale", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE, viridis.palette = "F") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - continuous variable legend position = top", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", continuous_feature = TRUE, legend.position = "top") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: FAIL - feature not found", { testthat::skip_on_cran() testthat::expect_error(SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "not_found", group.by = "seurat_clusters", continuous_feature = TRUE, viridis.palette = "F")) }) testthat::test_that("do_BeeSwarmPlot: PASS - raster", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", raster = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - colors.use", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", colors.use = c("0" = "#001219", "1" = "#005f73", "2" = "#0a9396", "3" = "#94d2bd", "4" = "#e9d8a6", "5" = "#ee9b00", "6" = "#ca6702", "7" = "#bb3e03", "8" = "#ae2012")) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - remove x axis", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", remove_x_axis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - remove y axis", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", remove_y_axis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - flip", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", flip = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - all NULL", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = NULL, flip = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - labs", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = NULL, xlab = "A", ylab = "B", flip = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = NULL, xlab = "A", ylab = "B", flip = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_BeeSwarmPlot: PASS - continuous feature cutoffs", { testthat::skip_on_cran() p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", flip = TRUE, continuous_feature = TRUE, min.cutoff = -1, max.cutoff = 1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", flip = TRUE, continuous_feature = TRUE, min.cutoff = -1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", flip = TRUE, continuous_feature = TRUE, max.cutoff = 1) testthat::expect_true(ggplot2::is_ggplot(p)) testthat::expect_error({ SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", flip = TRUE, continuous_feature = TRUE, max.cutoff = 2328443) }) testthat::expect_error({ SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", flip = TRUE, continuous_feature = TRUE, min.cutoff = -2328443) }) testthat::expect_error({ SCpubr::do_BeeSwarmPlot(sample = sample, feature_to_rank = "PC_1", group.by = "seurat_clusters", flip = TRUE, continuous_feature = TRUE, min.cutoff = 2328443, max.cutoff = -2328443) }) }) }