tests/testthat/test_clusterGeneSim.R

In llrs/BioCor: Functional similarities

test_that("clusterGeneSim", {
  expect_warning(
    test0 <- clusterGeneSim(c("2", "1"), c("9", "4"), info),
    "Using max method because after removing NAs"
  )
  expect_error(clusterGeneSim(c("2", "2"), c("4", "4"), info), "several")
  expect_error(clusterGeneSim(c("2", "2"), c(9, 4), info), "character")
  expect_error(
    clusterGeneSim(
      c("2", "2"), c("9", "4"),
      as.environment(info)
    ),
    "list"
  )
  expect_warning(test <- clusterGeneSim(c("13", "12"), c("9", "4"), info), "list")
  expect_true(is.na(test))
  expect_error(clusterGeneSim(c("2", "1"), c("9", "3"), info,
                              method = NULL
  ), "method")
  expect_warning(test2 <- clusterGeneSim(c("9", "4"), c("2", "1"), info))
  expect_equal(test0, 0.4)
  expect_equal(test0, test2)
  test <- clusterGeneSim(c("2", "1"), c("9", "4"), info, "max")
  expect_true(is.matrix(test))
  test <- clusterGeneSim(c("2", "1"), c("9", "4"), info, c("avg", "max"))
  expect_equal(test, 0.00909090909090909)
  test <- clusterGeneSim(c("2", "1"), c("9", "4"), info, c("avg", "max"),
                         round = TRUE
  )
  expect_equal(test, 0.009)
})

test_that("mclusterGeneSim", {
  expect_error(mclusterGeneSim(c("a", "b"), info), "list")
  expect_error(
    mclusterGeneSim(list(a = c("a", "b"), b = c(1, 2)), info),
    "character"
  )
  expect_error(
    mclusterGeneSim(list(a = c("a", "b")), info),
    "several clusters"
  )
  expect_error(mclusterGeneSim(clusters, c("a", "b")), "list")
  cluster2 <- clusters
  cluster2$cluster1 <- "199"
  expect_warning(mclusterGeneSim(cluster2, info), "not in")
  test <- mclusterGeneSim(clusters, info)
  expect_equal(test[1L, 1L], 1)

  test <- mclusterGeneSim(clusters, info, c("max", "avg"))
  expect_equal(test[1L, 1L], 1)
  expect_true(isSymmetric(test))
  expect_error(mclusterGeneSim(clusters, info, NULL))
})



test_that("clusterGeneSim GeneSetCollection", {
  expect_warning(test0 <- clusterGeneSim(c("2", "1"), c("9", "4"), info),
                 "Using max method because after removing NAs")
  expect_error(clusterGeneSim(c("2", "2"), c("4", "4"), info), "several")
  expect_error(clusterGeneSim(c("2", "2"), c(9, 4), info), "character")
  expect_warning(test <- clusterGeneSim(c("13", "12"), c("9", "4"), info),
                                "Some genes are not in the list provided")

  expect_true(is.na(test))
  expect_error(clusterGeneSim(c("2", "1"), c("9", "3"), info,
                                             method = NULL
  ), "method")
  expect_warning(test2 <- clusterGeneSim(c("9", "4"), c("2", "1"), info))
  expect_equal(test0, 0.4)
  expect_equal(test0, test2)
  test <- clusterGeneSim(c("2", "1"), c("9", "4"), info, "max")
  expect_true(is.matrix(test))
  test <- clusterGeneSim(c("2", "1"), c("9", "4"), info, c("avg", "max"))
  expect_lte(test, 0.01)
  test <- clusterGeneSim(c("2", "1"), c("9", "4"), info, c("avg", "max"),
                                        round = TRUE
  )
  expect_lte(test, 0.01)
})

test_that("mclusterGeneSim GeneSetCollection", {
  expect_error(mclusterGeneSim(c("a", "b"), info), "list")
  expect_error(
    mclusterGeneSim(list(a = c("a", "b"), b = c(1, 2)), info),
    "character"
  )
  expect_error(
    mclusterGeneSim(list(a = c("a", "b")), info),
    "several clusters"
  )
  expect_error(mclusterGeneSim(clusters, c("a", "b")), "list")
  cluster2 <- clusters
  cluster2$cluster1 <- "199"
  mclusterGeneSim(cluster2, info)
  test <- mclusterGeneSim(clusters, info)
  expect_equal(test[1L, 1L], 1)

  test <- mclusterGeneSim(clusters, info, c("max", "avg"))
  expect_equal(test[1L, 1L], 1)
  expect_true(isSymmetric(test))
  expect_error(expect_warning(mclusterGeneSim(clusters, info, NULL)))
})