tests/testthat/test_demonanalysis.R

In robjohnnoble/demonanalysis: Analysis and plotting of demon data

context("All tests")

library(ggmuller)
library(dplyr)

test_that("sweep sequences are consistent for proportions and breaks", {
  phylo <- filter(driver_phylo, CellsPerSample == -1)
  pop_df <- get_population_df(phylo)
  lag_gens <- round(length(unique(pop_df$Generation))/6)
  
  expect_equal(sweep_sequence(pop_df, lag_type = "proportions", breaks = 6), 
               sweep_sequence(pop_df, lag_type = "generations", lag_gens = lag_gens))
})

test_that("apply_combinations works for equal and unequal sequences", {
  expect_equal(sort(apply_combinations(c(2, 3), mean)), sort(apply_combinations(c(3, 2), mean)))
  expect_length(apply_combinations(c(2, 3), mean), 3*4)
  expect_length(apply_combinations(c(2, 2), mean), 3*3)
})

test_that("ancestry result has correct dimensions and NA counts", {
  edges1 <- data.frame(Parent = rep(0, 2), Identity = 1:2)
  anc <- ancestry(edges1)
  expect_equal(dim(anc)[1], 3)
  expect_equal(dim(anc)[2], 3)
  expect_equal(sum(is.na(anc)), 1)
})

test_that("dominant results", {
  edges1 <- data.frame(Parent = rep(0, 2), Identity = 1:2)
  anc <- ancestry(edges1)
  pop_df <- data.frame(Generation = rep(0:2, each = 3), 
                       Identity = rep(0:2, times = 3), 
                       Population = c(1, 0, 0, 2, 2, 0, 3, 5, 1))
  expect_equal(dominant(anc, pop_df, 0.1), 2)
  expect_equal(dominant(anc, pop_df, 0.5), 1)
  expect_equal(dominant(anc, pop_df, 0.5, 0), 0)
  expect_equal(dominant(anc, pop_df, 0, 0), 2)
})

test_that("find_correlations perfect fit", {
  s1 <- data.frame(a = 1:3, b = 1:3)
  expect_equal(find_correlations(s1, "a", "b", "c", 3)$c, 1)
})

test_that("combine_dfs() returns the desired output files", {
  full_dir <- system.file("extdata", "", package = "demonanalysis", mustWork = TRUE)
  # test dimensions output.dat
  expect_equal(dim(combine_dfs(full_dir = full_dir, include_diversities = TRUE)), c(32, 132))
  expect_equal(dim(combine_dfs(full_dir = full_dir, include_diversities = FALSE)), c(32, 57))
  
  # test driver_genotype_properties
  expect_equal(dim(combine_dfs(full_dir = full_dir, df_type = "driver_genotype_properties")), c(122,29))
  # with vaf_cut_off
  df_cut <- combine_dfs(full_dir = full_dir, df_type = "driver_genotype_properties", vaf_cut_off = 0.002)
  expect_equal(dim(df_cut), c(112,29))
  expect_equal(nrow(df_cut %>% filter(Population == 0, VAF < 0.002)), 0)

  # test genotype_properties
  expect_equal(dim(combine_dfs(full_dir = full_dir, df_type = "genotype_properties")), c(1219,29))
  df_cut <- combine_dfs(full_dir = full_dir, df_type = "genotype_properties", vaf_cut_off = 0.002)
  expect_equal(dim(df_cut), c(724,29))
  expect_equal(nrow(df_cut %>% filter(Population == 0, VAF < 0.002)), 0)
  
  # test wrong user input
  expect_error(combine_dfs(full_dir, df_type = "not a type"))
})

test_that("all_output() returns the desired output files", {
  input_dir <- system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE)
  all_output <- all_output(input_dir)
  expect_equal(dim(all_output), c(44,63))
  expect_equivalent(table(all_output$K, all_output$seed), as.table(matrix(c(11,11,11,11), nrow=2)))
  
  expect_equal(dim(all_output(input_dir, df_type = "driver_genotype_properties")), c(223, 31))
  df_cut <- all_output(input_dir, df_type = "driver_genotype_properties", vaf_cut_off = 0.002)
  expect_equal(dim(df_cut), c(222,31))
  expect_equal(nrow(df_cut %>% filter(Population == 0, VAF < 0.002)), 0)
  
  expect_equal(dim(all_output(input_dir, df_type = "genotype_properties")), c(457, 31))
  df_cut <- all_output(input_dir, df_type = "genotype_properties", vaf_cut_off = 0.002)
  expect_equal(dim(df_cut), c(427,31))
  expect_equal(nrow(df_cut %>% filter(Population == 0, VAF < 0.002)), 0)

  expect_error(all_output(input_dir, df_type = "not a type"))
})