tests/testthat/test-roxytest-testexamples-show_cn_group_profile.R

In ShixiangWang/sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

# Generated by roxytest: do not edit by hand!

# File R/show_cn_group_profile.R: @testexamples

test_that("Function show_cn_group_profile() @ L52", {
  
  load(system.file("extdata", "toy_copynumber.RData",
    package = "sigminer", mustWork = TRUE
  ))
  
  p1 <- show_cn_group_profile(cn)
  p1
  
  ss <- unique(cn@data$sample)
  p2 <- show_cn_group_profile(cn, groups = list(a = ss[1:5], b = ss[6:10]))
  p2
  p3 <- show_cn_group_profile(cn,
    groups = list(g1 = ss[1:5], g2 = ss[6:10]),
    force_y_limit = c(-1, 1), nrow = 2
  )
  p3
  
  ## Set custom cutoff for custom data
  data <- cn@data
  data$segVal <- data$segVal - 2L
  p4 <- show_cn_group_profile(data,
    groups = list(g1 = ss[1:5], g2 = ss[6:10]),
    force_y_limit = c(-1, 1), nrow = 2,
    cutoff = c(0, 0)
  )
  p4
  
  ## Add highlight gene
  p5 <- show_cn_group_profile(cn, highlight_genes = c("TP53", "EGFR"))
  p5
  
  expect_s3_class(p1, "ggplot")
  expect_s3_class(p2, "ggplot")
  expect_s3_class(p3, "ggplot")
  expect_s3_class(p4, "ggplot")
  expect_s3_class(p5, "ggplot")
})