if (base::isFALSE(dep_check[["do_EnrichmentHeatmap"]])){ testthat::test_that("do_EnrichmentHeatmap: CRAN essential", { sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B") genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) }) testthat::test_that("do_EnrichmentHeatmap: PASS -flavors", { testthat::skip_on_cran() genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, cluster = TRUE) testthat::expect_true("ggplot" %in% class(p)) genes <- list("A-A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) testthat::expect_warning(p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, cluster = TRUE, values.show = TRUE, values.threshold = 0.2)) testthat::expect_true("ggplot" %in% class(p)) genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, cluster = FALSE) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, cluster = TRUE, features.order = c("B", "A", "C")) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, cluster = TRUE, features.order = c("B", "A", "C"), groups.order = list("Groups" = c("1", "3", "5", "7", "0", "2", "4", "6", "8"))) testthat::expect_true("ggplot" %in% class(p)) genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = c("seurat_clusters", "orig.ident"), nbin = 1, ctrl = 10, enforce_symmetry = TRUE) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = c("seurat_clusters", "orig.ident"), nbin = 1, ctrl = 10, enforce_symmetry = FALSE, use_viridis = TRUE, viridis.direction = 1) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = c("seurat_clusters", "orig.ident"), nbin = 1, ctrl = 10, enforce_symmetry = FALSE, use_viridis = TRUE, viridis.direction = -1) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = c("seurat_clusters", "orig.ident"), nbin = 1, ctrl = 10, enforce_symmetry = FALSE, use_viridis = FALSE, sequential.direction = 1) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = c("seurat_clusters", "orig.ident"), nbin = 1, ctrl = 10, enforce_symmetry = FALSE, use_viridis = FALSE, sequential.direction = -1) testthat::expect_true("ggplot" %in% class(p)) genes <- list("A" = rownames(sample)[1:5]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, flip = FALSE) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, flip = TRUE) testthat::expect_true("ggplot" %in% class(p)) genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, features.order = c("A", "B", "C")) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, flavor = "Seurat", assay = "SCT", nbin = 1, ctrl = 10, viridis.direction = 1) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, flavor = "Seurat", assay = "SCT", nbin = 1, ctrl = 10, viridis.direction = -1) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, flavor = "UCell", slot = "data", nbin = 1, ctrl = 10, viridis.direction = 1) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, flavor = "UCell", slot = "data", nbin = 1, ctrl = 10, viridis.direction = -1) testthat::expect_true("ggplot" %in% class(p)) }) testthat::test_that("do_EnrichmentHeatmap: PASS - normal", { testthat::skip_on_cran() sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B") genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, legend.position = "top", nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, legend.position = "right", nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) }) testthat::test_that("do_EnrichmentHeatmap: PASS - group.by", { testthat::skip_on_cran() sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B") genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = "orig.ident", nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) }) testthat::test_that("do_EnrichmentHeatmap: PASS - group.by and flip", { testthat::skip_on_cran() sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B") genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = c("orig.ident", "seurat_clusters"), flip = TRUE, nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = "orig.ident", flip = TRUE, nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) }) testthat::test_that("do_EnrichmentHeatmap: PASS - character list of genes + group by only has 1 entity", { testthat::skip_on_cran() sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B") genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = "orig.ident", nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = c("seurat_clusters", "orig.ident"), nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = c("seurat_clusters", "orig.ident"), nbin = 1, ctrl = 10, return_object = TRUE) testthat::expect_true("list" %in% class(p)) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, nbin = 1, ctrl = 10, return_object = TRUE) testthat::expect_true("list" %in% class(p)) }) testthat::test_that("do_EnrichmentHeatmap: FAIL - list of genes without name", { testthat::skip_on_cran() sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B") genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) testthat::expect_error(SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = list("EPC1"), group.by = "orig.ident", nbin = 1, ctrl = 10)) testthat::expect_error(SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = list("A" = "EPC1"), group.by = "wrong", nbin = 1, ctrl = 10)) }) testthat::test_that("do_EnrichmentHeatmap: PASS - group by factor", { testthat::skip_on_cran() sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B") genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) sample$seurat_clusters.factor <- factor(sample$seurat_clusters) p <- SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, group.by = "seurat_clusters.factor", nbin = 1, ctrl = 10) testthat::expect_true("ggplot" %in% class(p)) }) testthat::test_that("do_EnrichmentHeatmap: ERROR - wrong arguments", { testthat::skip_on_cran() sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B") genes <- list("A" = rownames(sample)[1:5], "B" = rownames(sample)[6:10], "C" = rownames(sample)[11:15]) testthat::expect_warning({SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, flavor = "Seurat", slot = "data", nbin = 1, ctrl = 10)}) testthat::expect_warning({SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, flavor = "UCell", assay = "SCT", nbin = 1, ctrl = 10)}) testthat::expect_error({SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, min.cutoff = -10, nbin = 1, ctrl = 10)}) testthat::expect_error({SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, max.cutoff = 200, nbin = 1, ctrl = 10)}) testthat::expect_error({SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = genes, max.cutoff = 1, min.cutoff = 2, nbin = 1, ctrl = 10)}) testthat::expect_error({SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = list("A" = "EPC1"), group.by = c("seurat_clusters", "annotation"), nbin = 1, ctrl = 10, flip = FALSE, features.order = "wrong")}) testthat::expect_warning({SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = list("A_A" = "EPC1"), group.by = c("seurat_clusters", "annotation"), nbin = 1, ctrl = 10, flip = FALSE)}) testthat::expect_error({SCpubr::do_EnrichmentHeatmap(sample = sample, input_gene_list = "EPC1", nbin = 1, ctrl = 10)}) }) }