if (base::isFALSE(dep_check[["do_AlluvialPlot"]])){ testthat::test_that("do_AlluvialPlot: CRAN essential tests", { p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", last_group = "seurat_clusters") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_EnrichmentHeatmap: PASS - normal", { testthat::skip_on_cran() p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters") testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_labels = TRUE, repel = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_labels = TRUE, repel = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", flip = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", flip = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_viridis = TRUE, colors.use = NULL) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_labels = FALSE, repel = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", flip = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", flip = TRUE, use_labels = TRUE, repel = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", flip = TRUE, use_labels = TRUE, repel = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", flip = TRUE, use_labels = FALSE, repel = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", flip = TRUE, use_labels = FALSE, repel = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_AlluvialPlot: factors", { sample$orig.ident <- as.factor(sample$orig.ident) sample$seurat_clusters <- as.factor(sample$seurat_clusters) sample$annotation <- as.factor(sample$annotation) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters") testthat::expect_true(ggplot2::is_ggplot(p)) sample$orig.ident <- as.character(sample$orig.ident) sample$seurat_clusters <- as.character(sample$seurat_clusters) sample$annotation <- as.character(sample$annotation) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_AlluvialPlot: geom_flow", { p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_geom_flow = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_geom_flow = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_AlluvialPlot: stratum.fill.conditional", { p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_geom_flow = FALSE, stratum.fill.conditional = FALSE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_geom_flow = FALSE, stratum.fill.conditional = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_AlluvialPlot: use_viridis", { p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = "annotation", last_group = "seurat_clusters", use_geom_flow = FALSE, use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_AlluvialPlot: colors.use", { p <- SCpubr::do_AlluvialPlot(sample, first_group = "seurat_clusters", last_group = "orig.ident", colors.use = c("Cell" = "blue")) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_AlluvialPlot: test_numbers", { sample$annotation2 <- sample$annotation sample$annotation3 <- sample$annotation sample$annotation4 <- sample$annotation sample$annotation5 <- sample$annotation sample$annotation6 <- sample$annotation sample$annotation7 <- sample$annotation sample$annotation8 <- sample$annotation p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = c("annotation", "annotation2"), last_group = "seurat_clusters", use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = c("annotation", "annotation2", "annotation3"), last_group = "seurat_clusters", use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = c("annotation", "annotation2", "annotation3", "annotation4"), last_group = "seurat_clusters", use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = c("annotation", "annotation2", "annotation3", "annotation4", "annotation5"), last_group = "seurat_clusters", use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = c("annotation", "annotation2", "annotation3", "annotation4", "annotation5", "annotation6"), last_group = "seurat_clusters", use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = c("annotation", "annotation2", "annotation3", "annotation4", "annotation5", "annotation6", "annotation7"), last_group = "seurat_clusters", use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_AlluvialPlot(sample, first_group = "orig.ident", middle_groups = c("annotation", "annotation2", "annotation3", "annotation4", "annotation5", "annotation6", "annotation7", "annotation8"), last_group = "seurat_clusters", use_viridis = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) }