if (base::isFALSE(dep_check[["do_PathwayActivityHeatmap"]])){ testthat::test_that("do_PathwayActivityHeatmap: CRAN essentials", { out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities) testthat::expect_type(out, "list") }) testthat::test_that("do_PathwayActivityHeatmap: PASS - minimal input", { testthat::skip_on_cran() sample$annotation <- sample(c("A", "B"), ncol(sample), replace = TRUE) out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, values.show = TRUE, values.threshold = 0.2) testthat::expect_type(out, "list") sample$annotation <- sample(c("A", "B"), ncol(sample), replace = TRUE) out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, enforce_symmetry = TRUE) testthat::expect_type(out, "list") sample$annotation <- sample(c("A", "B"), ncol(sample), replace = TRUE) out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, enforce_symmetry = FALSE) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, group.by = "orig.ident") testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, group.by = c("orig.ident", "seurat_clusters", "annotation")) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, split.by = "annotation") testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, flip = TRUE) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, flip = FALSE) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, legend.position = "right") testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, legend.position = "right", return_object = TRUE) testthat::expect_type(out, "list") }) testthat::test_that("do_PathwayActivityHeatmap: PASS - all group.by", { testthat::skip_on_cran() out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, group.by = "orig.ident") testthat::expect_type(out, "list") }) testthat::test_that("do_PathwayActivityHeatmap: PASS - all split.by 2", { testthat::skip_on_cran() out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, min.cutoff = -0.1, max.cutoff = NA) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, min.cutoff = NA, max.cutoff = 0.1) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, min.cutoff = -0.1) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, max.cutoff = 0.1) testthat::expect_type(out, "list") out <- SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, max.cutoff = 0.1, min.cutoff = -0.1) testthat::expect_type(out, "list") }) testthat::test_that("do_PathwayActivityHeatmap: FAIL", { testthat::skip_on_cran() testthat::expect_error({SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, min.cutoff = -10)}) testthat::expect_error({SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, max.cutoff = 200)}) testthat::expect_error({SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, max.cutoff = 1, min.cutoff = 2)}) sample$annotation <- sample(c("A", "B"), ncol(sample), replace = TRUE) testthat::expect_error({SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities, group.by = c("seurat_clusters", "orig.ident"), split.by = "annotation")}) }) }