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
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
context("test-plot_rainfall")
# Read data
vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
package = "MutationalPatterns"
))
grl_indel_context <- readRDS(system.file("states/blood_grl_indel_context.rds",
package = "MutationalPatterns"
))
grl_dbs_context <- readRDS(system.file("states/blood_grl_dbs_context.rds",
package = "MutationalPatterns"
))
mbs_grl <- readRDS(system.file("states/blood_grl_mbs.rds",
package = "MutationalPatterns"
))
# Specify chromosomes of interest.
chromosomes <- paste0("chr", c(1:22))
# Do a rainfall plot for all chromosomes:
output <- plot_rainfall(vcfs[[1]], title = names(vcfs[1]), chromosomes = chromosomes)
# Plot a single chromosome (chromosome 1):
output_singlechrom <- plot_rainfall(vcfs[[1]], title = names(vcfs[1]), chromosomes = chromosomes[1])
# Plot a subset of the variants
output_subset <- plot_rainfall(vcfs[[1]][1:10], title = names(vcfs[1]), chromosomes = chromosomes)
# plot indels
output_indel <- plot_rainfall(grl_indel_context[[1]], title = names(grl_indel_context[1]), chromosomes = chromosomes, type = "indel")
# plot dbs
output_dbs <- plot_rainfall(grl_dbs_context[[1]], title = names(grl_dbs_context[1]), chromosomes = chromosomes, type = "dbs")
# plot mbs
output_mbs <- plot_rainfall(mbs_grl[[1]], title = names(mbs_grl[1]), chromosomes = chromosomes, type = "mbs")
# Plot an empty gr
output_empty <- plot_rainfall(vcfs[[1]][0], title = names(vcfs[1]), chromosomes = chromosomes)
test_that("Output has correct class", {
expect_true(inherits(output, c("gg")))
expect_true(inherits(output_singlechrom, c("gg")))
expect_true(inherits(output_subset, c("gg")))
expect_true(inherits(output_indel, c("gg")))
expect_true(inherits(output_dbs, c("gg")))
expect_true(inherits(output_mbs, c("gg")))
expect_true(inherits(output_empty, c("gg")))
})
test_that("Subsetted output contains the correct subset of colours", {
colours_used <- unique(ggplot_build(output_subset)$data[[1]][["colour"]])
expect_equal(colours_used, c("#ADCC54", "#DE1C14", "#2EBAED", "#D4D2D2"))
})
|
