tests/testthat/test-do_CellularStatesPlot.R
In enblacar/SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data
if (base::isFALSE(dep_check[["do_CellularStatesPlot"]])){
testthat::test_that("do_CellularStatesPlot: CRAN essentials", {
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
raster = TRUE,
pt.size = 1,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - cell_borders", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
raster = TRUE,
pt.size = 1,
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
raster = TRUE,
pt.size = 1,
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
raster = TRUE,
pt.size = 1,
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - continuous feature", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = FALSE,
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables marginal", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables marginal marginal.size", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.size = 8,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables marginal marginal.group FALSE", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.group = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables marginal distribution types", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.type = "density",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.type = "histogram",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.type = "boxplot",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.type = "violin",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
#p <- SCpubr::do_CellularStatesPlot(sample = sample,
# input_gene_list = genes,
# x1 = "A",
# y1 = "B",
# plot_marginal_distributions = TRUE,
# plot_cell_borders = FALSE,
# marginal.type = "densigram",
# nbin = 1,
# ctrl = 10)
#testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables marginal wrong marginal.type", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error({SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
marginal.type = "wrong",
nbin = 1,
ctrl = 10)})
})
testthat::test_that("do_CellularStatesPlot: PASS - title, subtitle and caption", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot.title = "A",
plot.subtitle = "B",
plot.caption = "C",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables enforce symmetry", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables, colors.use", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
Seurat::Idents(sample) <- sample$orig.ident
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
colors.use = c("A" = "black", "B" = "red"),
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables, group.by", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
group.by = "orig.ident",
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables remove axis ticks", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
axis.ticks = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables remove axis text", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
axis.text = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables, group.by and colors.use", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
group.by = "orig.ident",
colors.use = c("A" = "black", "B" = "red"),
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables same parameters", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "A",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables x1 not in the list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "Not in list",
y1 = "A",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables y1 not in the list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "Not in list",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables provide features", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_features = TRUE,
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: PASS - 3 variables", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
raster = TRUE,
pt.size = 1,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 3 variables marginal", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 3 variables enforce symmetry", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: FAIL - 3 variables duplicated parameters", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "A",
x2 = "B",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 3 variables x1 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "Not in list",
y1 = "A",
x2 = "B",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 3 variables x2 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "B",
y1 = "A",
x2 = "Not in list",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 3 variables y1 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "Not in list",
x2 = "B",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: PASS - 4 variables", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
raster = TRUE,
pt.size = 1,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 4 variables marginal", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 4 variables enforce symmetry", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables repeated parameters", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "A",
x2 = "A",
y2 = "A",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables x1 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "Not in list",
y1 = "B",
x2 = "C",
y2 = "D",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables y1 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "Not in list",
x2 = "C",
y2 = "D",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables x2 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "Not in list",
y2 = "D",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables y2 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "Not in list",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - wrong font.type", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "Not in list",
x2 = "B",
font.type = "wrong",
nbin = 1,
ctrl = 10))
})
}
enblacar/SCpubr documentation built on Aug. 25, 2024, 9:45 p.m.
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if (base::isFALSE(dep_check[["do_CellularStatesPlot"]])){
testthat::test_that("do_CellularStatesPlot: CRAN essentials", {
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
raster = TRUE,
pt.size = 1,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - cell_borders", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
raster = TRUE,
pt.size = 1,
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
raster = TRUE,
pt.size = 1,
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
raster = TRUE,
pt.size = 1,
plot_cell_borders = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - continuous feature", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = TRUE,
features = "EPC1",
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_cell_borders = TRUE,
plot_features = FALSE,
plot_enrichment_scores = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables marginal", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables marginal marginal.size", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.size = 8,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables marginal marginal.group FALSE", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.group = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables marginal distribution types", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.type = "density",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.type = "histogram",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.type = "boxplot",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
marginal.type = "violin",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
#p <- SCpubr::do_CellularStatesPlot(sample = sample,
# input_gene_list = genes,
# x1 = "A",
# y1 = "B",
# plot_marginal_distributions = TRUE,
# plot_cell_borders = FALSE,
# marginal.type = "densigram",
# nbin = 1,
# ctrl = 10)
#testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables marginal wrong marginal.type", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error({SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_marginal_distributions = TRUE,
marginal.type = "wrong",
nbin = 1,
ctrl = 10)})
})
testthat::test_that("do_CellularStatesPlot: PASS - title, subtitle and caption", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot.title = "A",
plot.subtitle = "B",
plot.caption = "C",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables enforce symmetry", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables, colors.use", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
Seurat::Idents(sample) <- sample$orig.ident
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
colors.use = c("A" = "black", "B" = "red"),
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables, group.by", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
group.by = "orig.ident",
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables remove axis ticks", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
axis.ticks = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables remove axis text", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
axis.text = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 2 variables, group.by and colors.use", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
group.by = "orig.ident",
colors.use = c("A" = "black", "B" = "red"),
x1 = "A",
y1 = "B",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables same parameters", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "A",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables x1 not in the list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "Not in list",
y1 = "A",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables y1 not in the list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "Not in list",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 2 variables provide features", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
plot_features = TRUE,
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: PASS - 3 variables", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
raster = TRUE,
pt.size = 1,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 3 variables marginal", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 3 variables enforce symmetry", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: FAIL - 3 variables duplicated parameters", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "A",
x2 = "B",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 3 variables x1 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "Not in list",
y1 = "A",
x2 = "B",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 3 variables x2 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "B",
y1 = "A",
x2 = "Not in list",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 3 variables y1 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "Not in list",
x2 = "B",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: PASS - 4 variables", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
raster = TRUE,
pt.size = 1,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 4 variables marginal", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
plot_marginal_distributions = TRUE,
plot_cell_borders = FALSE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: PASS - 4 variables enforce symmetry", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
p <- SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "D",
enforce_symmetry = TRUE,
nbin = 1,
ctrl = 10)
testthat::expect_type(p, "list")
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables repeated parameters", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "A",
x2 = "A",
y2 = "A",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables x1 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "Not in list",
y1 = "B",
x2 = "C",
y2 = "D",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables y1 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "Not in list",
x2 = "C",
y2 = "D",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables x2 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "Not in list",
y2 = "D",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - 4 variables y2 not in list", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "B",
x2 = "C",
y2 = "Not in list",
nbin = 1,
ctrl = 10))
})
testthat::test_that("do_CellularStatesPlot: FAIL - wrong font.type", {
testthat::skip_on_cran()
sample$orig.ident <- ifelse(sample$seurat_clusters %in% c("1", "2"), "A", "B")
genes <- list("A" = Seurat::VariableFeatures(sample)[1:5],
"B" = Seurat::VariableFeatures(sample)[6:10],
"C" = Seurat::VariableFeatures(sample)[11:15],
"D" = Seurat::VariableFeatures(sample)[16:20])
testthat::expect_error(SCpubr::do_CellularStatesPlot(sample = sample,
input_gene_list = genes,
x1 = "A",
y1 = "Not in list",
x2 = "B",
font.type = "wrong",
nbin = 1,
ctrl = 10))
})
}
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