1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
|
context("test-plot_enrichment_depletion")
# Read distribution data
distr <- readRDS(system.file("states/distr_data.rds",
package = "MutationalPatterns"
))
# Set tissue
tissue <- c(
"colon", "colon", "colon",
"intestine", "intestine", "intestine",
"liver", "liver", "liver"
)
## Perform the enrichment/depletion test.
distr_test <- enrichment_depletion_test(distr, by = tissue)
distr_test2 <- enrichment_depletion_test(distr)
## Plot the enrichment/depletion
output <- plot_enrichment_depletion(distr_test)
output_persample <- plot_enrichment_depletion(distr_test2)
## Test with p instead of fdr
output_pval <- plot_enrichment_depletion(distr_test, sig_type = "p")
## Use multiple (max 3) significance cutoffs.
distr_multistars <- enrichment_depletion_test(distr,
by = tissue,
p_cutoffs = c(0.05, 0.01, 0.005),
fdr_cutoffs = c(0.1, 0.05, 0.01)
)
output_multistars <- plot_enrichment_depletion(distr_multistars)
# Perform tests
test_that("Output has correct class", {
expect_true(inherits(output, c("gg")))
expect_true(inherits(output_persample, c("gg")))
expect_true(inherits(output_pval, c("gg")))
expect_true(inherits(output_multistars, c("gg")))
})
|
