tests/testthat/test-celda-functions.R

In campbio/celda: CEllular Latent Dirichlet Allocation

# library(celda)
# context("Testing miscellaneous celda functions")
#
# data(celdaCGGridSearchRes)
# celdaCGSim <- simulateCells("celda_CG", K = 5, L = 10)
# modelCG <- celda_CG(
#     counts = celdaCGSim$counts,
#     sampleLabel = celdaCGSim$sampleLabel,
#     K = celdaCGSim$K,
#     L = celdaCGSim$L,
#     algorithm = "EM",
#     verbose = FALSE,
#     nchains = 1)
#
# factorized <- factorizeMatrix(celdaMod = modelCG, counts = celdaCGSim$counts)
#
# test_that(desc = "Testing compareCountMatrix with numeric matrix input", {
#     # Case from GitHub issue #137
#     counts <- celdaCGSim$counts
#     storage.mode(counts) <- "numeric"
#     expect_true(compareCountMatrix(counts, modelCG, errorOnMismatch = TRUE))
# })
#
# test_that(desc = "Testing appendCeldaList", {
#     expect_error(
#         appendCeldaList(celdaCGGridSearchRes, matrix(0)),
#         "Both parameters to appendCeldaList must be of class celdaList."
#     )
#     modifiedEgList <- celdaCGGridSearchRes
#     modifiedEgList@countChecksum <- "abcd12345"
#     expect_warning(
#         appendCeldaList(celdaCGGridSearchRes, modifiedEgList),
#         paste0("Provided lists have different countChecksums and may have",
#         " been generated from different count matrices. Using checksum",
#         " from first list..."))
#     expect_equal(length(celdaCGGridSearchRes@resList) * 2,
#         length(appendCeldaList(celdaCGGridSearchRes,
#             celdaCGGridSearchRes)@resList))
# })


# miscellaneous fxns
# functions used internally
test_that(desc = "Invoking error from distinctColors function", {
  expect_error(distinctColors(n = 3, hues = "xx"),
               paste0("Only color names listed in the 'color' function can be",
                      " used in 'hues'"))
})

test_that(desc = "Invoking error from sample labels function", {
  expect_error(.processSampleLabels("Sample_1", 5),
               paste0("'sampleLabel' must be the same length as the number",
                      " of columns in the 'counts' matrix."))
})

test_that(desc = "Invoking error from .logMessages function", {
  expect_error(.logMessages(date(), logfile = 5))
})

test_that(desc = paste0("miscellaneous distance fxns that are not directly",
                        " used within celda, but will be tested"), {
                          x <- data.frame(x = seq(2, 4), y = seq(1, 3))
                          expect_equal(class(.hellingerDist(x)), "dist")
                          expect_equal(class(.spearmanDist(x)), "dist")
                        })