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context("test-plot_strand_bias")
# Read stranded mut_mat
mut_mat_s <- readRDS(system.file("states/mut_mat_s_data.rds",
package = "MutationalPatterns"
))
tissue <- c(
"colon", "colon", "colon",
"intestine", "intestine", "intestine",
"liver", "liver", "liver"
)
## Perform the strand bias test.
strand_counts <- strand_occurrences(mut_mat_s, by = tissue)
strand_bias <- strand_bias_test(strand_counts)
## Plot the strand bias.
output <- plot_strand_bias(strand_bias)
# Repeat for replication bias.
mut_mat_repli <- readRDS(system.file("states/mut_mat_repli.rds",
package = "MutationalPatterns"
))
strand_counts <- strand_occurrences(mut_mat_repli, by = tissue)
strand_bias <- strand_bias_test(strand_counts)
output_repli <- plot_strand_bias(strand_bias)
## Test with p instead of fdr
output_pval <- plot_strand_bias(strand_bias, sig_type = "p")
## Use multiple (max 3) significance cutoffs.
strand_bias_multistars <- strand_bias_test(strand_counts,
p_cutoffs = c(0.05, 0.01, 0.005),
fdr_cutoffs = c(0.1, 0.05, 0.01)
)
output_multistars <- plot_strand_bias(strand_bias_multistars)
test_that("Output has correct class", {
expect_true(inherits(output, c("gg")))
expect_true(inherits(output_repli, c("gg")))
expect_true(inherits(output_pval, c("gg")))
expect_true(inherits(output_multistars, c("gg")))
})
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