if(base::isFALSE(dep_check[["do_NebulosaPlot"]])){ testthat::test_that("do_NebulosaPlot: CRAN essentials", { p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1") testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2")) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), joint = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - single feature", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", use_viridis = TRUE, viridis.direction = 1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", use_viridis = TRUE, viridis.direction = -1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", use_viridis = FALSE, sequential.direction = 1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", use_viridis = FALSE, sequential.direction = -1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), use_viridis = TRUE, viridis.direction = 1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), use_viridis = TRUE, viridis.direction = -1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), use_viridis = FALSE, sequential.direction = 1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), use_viridis = FALSE, sequential.direction = -1) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), use_viridis = TRUE, viridis.direction = 1, joint = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), use_viridis = TRUE, viridis.direction = -1, joint = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), use_viridis = FALSE, sequential.direction = 1, joint = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "TOX2"), use_viridis = FALSE, sequential.direction = -1, joint = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - cell_borders", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", plot_cell_borders = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) p <- suppressWarnings({SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "PC_1"), plot_cell_borders = TRUE)}) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - single feature legend normal", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", legend.type = "normal") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - single feature legend colorbar", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", legend.type = "colorbar") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: FAIL - wrong legend type ", { testthat::skip_on_cran() testthat::expect_error(SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", legend.type = "wrong")) }) testthat::test_that("do_NebulosaPlot: FAIL - wrong legend position ", { testthat::skip_on_cran() testthat::expect_error(SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", legend.position = "wrong")) }) testthat::test_that("do_NebulosaPlot: FAIL - wrong font.type", { testthat::skip_on_cran() testthat::expect_error(SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", font.type = "wrong")) }) testthat::test_that("do_NebulosaPlot: PASS - single feature distinct dims", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", dims = c(2, 1)) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_FeaturePlot: PASS - diffusion", { testthat::skip_on_cran() test <- sample@reductions$umap[[]] colnames(test) <- c("DC_1", "DC_2") obj <- Seurat::CreateDimReducObject(test, assay = "SCT", key = "DC_") sample@reductions$diffusion <- obj p <- suppressWarnings(SCpubr::do_NebulosaPlot(sample, features = "PC_1", reduction = "diffusion")) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - several", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "LTV1")) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - several, joint", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "LTV1"), joint = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - several, joint only joint", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "LTV1"), joint = TRUE, return_only_joint = TRUE) testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - title", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "LTV1"), joint = TRUE, return_only_joint = TRUE, plot.title = "Title") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - subtitle", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "LTV1"), joint = TRUE, return_only_joint = TRUE, plot.subtitle = "Subtitle") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - caption", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "LTV1"), joint = TRUE, return_only_joint = TRUE, plot.caption = "Caption") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - color map", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", viridis.palette = "F") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - legend top", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", legend.position = "left") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - legend top", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", legend.position = "top") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: WARNING - features as list", { testthat::skip_on_cran() testthat::expect_warning(SCpubr::do_NebulosaPlot(sample = sample, features = list("EPC1"), viridis.palette = "F")) }) testthat::test_that("do_NebulosaPlot: PASS - no legend", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1", legend.position = "none") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - patchwork title, subtitle and caption", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, features = c("EPC1", "LTV1"), plot.title = "A", plot.subtitle = "B", plot.caption = "C") testthat::expect_true(ggplot2::is_ggplot(p)) }) testthat::test_that("do_NebulosaPlot: PASS - plot axis", { testthat::skip_on_cran() p <- SCpubr::do_NebulosaPlot(sample = sample, plot.axes = TRUE, features = "nCount_RNA") testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, reduction = "pca", plot.axes = TRUE, features = "nCount_RNA") testthat::expect_true(ggplot2::is_ggplot(p)) p <- SCpubr::do_NebulosaPlot(sample = sample, dims = c(2, 1), plot.axes = TRUE, features = "nCount_RNA") testthat::expect_true(ggplot2::is_ggplot(p)) sample@reductions$diffusion <- sample@reductions$umap p <- SCpubr::do_NebulosaPlot(sample = sample, reduction = "diffusion", plot.axes = TRUE, features = "nCount_RNA") testthat::expect_true(ggplot2::is_ggplot(p)) }) }