data("gene_expression", package = "ggpubr")
data("ToothGrowth")
test_that("compare_means works for One-sample test", {
results <- compare_means(len ~ 1, ToothGrowth, mu = 0)
results <- results %>%
dplyr::select(.y., group1, group2, p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~group1, ~group2, ~p.format, ~p.signif, ~method,
"len", 1, "null model", "1.7e-11", "****", "Wilcoxon"
)
expect_equal(results, expected)
})
test_that("compare_means works for Two-samples unpaired test", {
results <- compare_means(len ~ supp, ToothGrowth)
results <- results %>%
dplyr::select(.y., group1, group2, p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~group1, ~group2, ~p.format, ~p.signif, ~method,
"len", "OJ", "VC", "0.064", "ns", "Wilcoxon"
)
expect_equal(results, expected)
})
test_that("compare_means works for Two-samples paired test", {
results <- compare_means(len ~ supp, ToothGrowth, paired = TRUE)
results <- results %>%
dplyr::select(.y., group1, group2, p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~group1, ~group2, ~p.format, ~p.signif, ~method,
"len", "OJ", "VC", "0.0043", "**", "Wilcoxon"
)
expect_equal(results, expected)
})
test_that("compare_means works for pairwise comparisons", {
results <- compare_means(len ~ dose, ToothGrowth)
results <- results %>%
dplyr::select(.y., group1, group2, p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~group1, ~group2, ~p.format, ~p.signif, ~method,
"len", "0.5", "1", "7.0e-06", "****", "Wilcoxon",
"len", "0.5", "2", "8.4e-08", "****", "Wilcoxon",
"len", "1", "2", "0.00018", "***", "Wilcoxon"
)
expect_equal(results, expected)
})
test_that("compare_means works for comparison against reference groups", {
results <- compare_means(len ~ dose, ToothGrowth, ref.group = "0.5")
results <- results %>%
dplyr::select(.y., group1, group2, p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~group1, ~group2, ~p.format, ~p.signif, ~method,
"len", "0.5", "1", "7.0e-06", "****", "Wilcoxon",
"len", "0.5", "2", "8.4e-08", "****", "Wilcoxon"
)
expect_equal(results, expected)
})
test_that("compare_means works when using formula with multiple variables", {
results <- compare_means(c(GATA3, XBP1, PTEN) ~ dataset, data = gene_expression)
results <- results %>%
dplyr::select(.y., group1, group2, p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~group1, ~group2, ~p.format, ~p.signif, ~method,
"GATA3", "BRCA", "OV", "< 2e-16", "****", "Wilcoxon",
"GATA3", "BRCA", "LUSC", "< 2e-16", "****", "Wilcoxon",
"GATA3", "OV", "LUSC", "3.0e-08", "****", "Wilcoxon",
"XBP1", "BRCA", "OV", "< 2e-16", "****", "Wilcoxon",
"XBP1", "BRCA", "LUSC", "< 2e-16", "****", "Wilcoxon",
"XBP1", "OV", "LUSC", "4.2e-11", "****", "Wilcoxon",
"PTEN", "BRCA", "OV", "6.8e-05", "****", "Wilcoxon",
"PTEN", "BRCA", "LUSC", "< 2e-16", "****", "Wilcoxon",
"PTEN", "OV", "LUSC", "1.3e-07", "****", "Wilcoxon"
) %>%
dplyr::mutate(.y. = factor(.y., levels = c("GATA3", "XBP1", "PTEN")))
expect_equal(results, expected)
})
test_that("compare_means works when using ref.group = '.all.'", {
results <- compare_means(len ~ dose, ToothGrowth, ref.group = ".all.")
results <- results %>%
dplyr::select(.y., group1, group2, p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~group1, ~group2, ~p.format, ~p.signif, ~method,
"len", ".all.", "0.5", "5.1e-05", "****", "Wilcoxon",
"len", ".all.", "1", "0.76404", "ns", "Wilcoxon",
"len", ".all.", "2", "0.00018", "***", "Wilcoxon"
)
expect_equal(results, expected)
})
test_that("compare_means works for Anova", {
results <- compare_means(len ~ dose, ToothGrowth, method = "anova")
results <- results %>%
dplyr::select(.y., p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~p.format, ~p.signif, ~method,
"len", "9.5e-16", "****", "Anova"
)
expect_equal(results, expected)
})
test_that("compare_means works for kruskal.test", {
results <- compare_means(len ~ dose, ToothGrowth, method = "kruskal.test")
results <- results %>%
dplyr::select(.y., p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~p.format, ~p.signif, ~method,
"len", "1.5e-09", "****", "Kruskal-Wallis"
)
expect_equal(results, expected)
})
test_that("compare_means works when grouping variable levels contain group2", {
tibble::tribble(
~val, ~gp, ~by,
923 , 'group4','V1',
1252, 'group4','V1',
1442, 'group4','V1',
1398, 'group2','V1',
1858, 'group2','V1',
1330, 'group2','V1',
2593, 'group2','V1',
23 , 'group4','V2',
252, 'group4','V2',
442, 'group4','V2',
398, 'group2','V2',
858, 'group2','V2',
330, 'group2','V2',
593, 'group2','V2'
) %>% dplyr::mutate(gp=factor(gp, levels = c('group2','group4'))) -> dat
results <- compare_means(val ~ gp, data = dat, group.by = 'by', paired = F)
results <- results %>%
dplyr::select(.y., group1, group2, p.format, p.signif, method)
expected <- tibble::tribble(
~.y., ~group1, ~group2, ~p.format, ~p.signif, ~method,
"val", "group2", "group4", "0.23", "ns", "Wilcoxon",
"val", "group2", "group4", "0.23", "ns", "Wilcoxon"
)
expect_equal(results, expected)
})
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