tests/testthat/test-do_AffinityAnalysisPlot.R
In enblacar/SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data
if (base::isFALSE(dep_check[["do_AffinityAnalysisPlot"]])){
testthat::test_that("do_AffinityAnalysisPlot: CRAN essentials", {
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = NA,
nbin = 1,
ctrl = 5,
verbose = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - default", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = TRUE)
testthat::expect_type(p, "list")
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:11],
"C" = rownames(sample)[12:19])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = FALSE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
group.by = c("seurat_clusters", "orig.ident"),
flip = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
group.by = c("seurat_clusters", "orig.ident"),
flip = FALSE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
group.by = c("seurat_clusters", "orig.ident"),
flip = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
group.by = c("seurat_clusters", "orig.ident"),
flip = FALSE)
testthat::expect_type(p, "list")
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = TRUE,
return_object = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - robustness", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = FALSE)
testthat::expect_type(p, "list")
suppressMessages({testthat::expect_message({p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = TRUE,
flip = TRUE)})})
testthat::expect_type(p, "list")
genes <- list("A" = rownames(sample)[1:3],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[9:15])
testthat::expect_error({SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)})
genes <- list("A" = rownames(sample)[1:15],
"B" = rownames(sample)[16:40],
"C" = rownames(sample)[41:80])
SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - symmetry", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
enforce_symmetry = FALSE,
use_viridis = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
enforce_symmetry = FALSE,
use_viridis = FALSE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
enforce_symmetry = TRUE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - add enrichment", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
use_viridis = TRUE,
flip = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
use_viridis = TRUE,
flip = FALSE)
testthat::expect_type(p, "list")
suppressMessages({testthat::expect_message({ p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = TRUE,
use_viridis = TRUE)})})
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
use_viridis = TRUE,
flavor = "UCell")
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
use_viridis = FALSE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
enforce_symmetry = TRUE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - flip", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - cutoffs", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
min.cutoff = -0.25,
max.cutoff = 0.25)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - multiple group.by", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
group.by = c("seurat_clusters", "orig.ident"),
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - verbose", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
testthat::expect_message({p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = TRUE)})
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - underscores", {
testthat::skip_on_cran()
genes <- list("_A" = rownames(sample)[1:5],
"_B" = rownames(sample)[6:10],
"_C" = rownames(sample)[11:15])
testthat::expect_warning({p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)})
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - different length of gene sets", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:15],
"C" = rownames(sample)[15:30])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)
testthat::expect_type(p, "list")
})
}
enblacar/SCpubr documentation built on Aug. 25, 2024, 9:45 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
if (base::isFALSE(dep_check[["do_AffinityAnalysisPlot"]])){
testthat::test_that("do_AffinityAnalysisPlot: CRAN essentials", {
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = NA,
nbin = 1,
ctrl = 5,
verbose = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - default", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = TRUE)
testthat::expect_type(p, "list")
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:11],
"C" = rownames(sample)[12:19])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = FALSE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
group.by = c("seurat_clusters", "orig.ident"),
flip = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
group.by = c("seurat_clusters", "orig.ident"),
flip = FALSE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
group.by = c("seurat_clusters", "orig.ident"),
flip = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
group.by = c("seurat_clusters", "orig.ident"),
flip = FALSE)
testthat::expect_type(p, "list")
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = TRUE,
return_object = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - robustness", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = FALSE)
testthat::expect_type(p, "list")
suppressMessages({testthat::expect_message({p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = TRUE,
flip = TRUE)})})
testthat::expect_type(p, "list")
genes <- list("A" = rownames(sample)[1:3],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[9:15])
testthat::expect_error({SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)})
genes <- list("A" = rownames(sample)[1:15],
"B" = rownames(sample)[16:40],
"C" = rownames(sample)[41:80])
SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - symmetry", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
enforce_symmetry = FALSE,
use_viridis = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
enforce_symmetry = FALSE,
use_viridis = FALSE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
enforce_symmetry = TRUE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - add enrichment", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
use_viridis = TRUE,
flip = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
use_viridis = TRUE,
flip = FALSE)
testthat::expect_type(p, "list")
suppressMessages({testthat::expect_message({ p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = TRUE,
use_viridis = TRUE)})})
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
use_viridis = TRUE,
flavor = "UCell")
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
use_viridis = FALSE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
enforce_symmetry = TRUE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - flip", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = TRUE)
testthat::expect_type(p, "list")
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
flip = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - cutoffs", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE,
min.cutoff = -0.25,
max.cutoff = 0.25)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - multiple group.by", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
group.by = c("seurat_clusters", "orig.ident"),
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - verbose", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:10],
"C" = rownames(sample)[11:15])
testthat::expect_message({p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = TRUE)})
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - underscores", {
testthat::skip_on_cran()
genes <- list("_A" = rownames(sample)[1:5],
"_B" = rownames(sample)[6:10],
"_C" = rownames(sample)[11:15])
testthat::expect_warning({p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)})
testthat::expect_type(p, "list")
})
testthat::test_that("do_AffinityAnalysisPlot: PASS - different length of gene sets", {
testthat::skip_on_cran()
genes <- list("A" = rownames(sample)[1:5],
"B" = rownames(sample)[6:15],
"C" = rownames(sample)[15:30])
p <- SCpubr::do_AffinityAnalysisPlot(sample = sample,
input_gene_list = genes,
subsample = 100,
nbin = 1,
ctrl = 5,
verbose = FALSE)
testthat::expect_type(p, "list")
})
}
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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