tests/testthat/test_dispersion_est.R

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

context('seqData dispersion_est')

test_that('dispersion_est returns the correct data frame and attributes', {
  # Load the reduced peptide data frames ---------------------------------------

  load(system.file('testdata',
    'little_seqdata.RData',
    package = 'pmartR'
  ))

  # Run as.seqData with agreeable data frames ----------------------------------

  # Construct a seqData object with the edata, fdata, and emeta data frames.
  seqdata <- as.seqData(
    e_data = edata,
    f_data = fdata,
    edata_cname = 'ID_REF',
    fdata_cname = 'Samples'
  )

  expect_error(
    dispersion_est(seqdata, method = "edgeR"),
    "OmicsData requires group_designation for statistical analysis"
  )

  seqdata_grp <- group_designation(seqdata, main_effects = c("Tissue", "Treatment"))

  expect_error(
    dispersion_est(seqdata_grp, method = "fhk"),
    "method must a single character string of length 1 in 'edgeR', 'DESeq2', or 'voom'"
  )

  expect_error(
    dispersion_est(seqdata_grp$f_data, method = "edgeR"),
    "omicsData must be of class 'seqData'"
  )

  edgeR_res <- dispersion_est(seqdata_grp, method = "edgeR")
  deseq2_res <- suppressWarnings(dispersion_est(seqdata_grp, method = "DESeq2"))
  voom_res <- dispersion_est(seqdata_grp, method = "voom")

  res <- purrr::map(list(edgeR_res, deseq2_res, voom_res), function(gg) {
    expect_true(inherits(gg, "ggplot"))
  })

  ## Custom theme warning/error
  edgeR_res <- expect_error(
    expect_warning(
      dispersion_est(seqdata_grp, method = "edgeR", bw_theme = TRUE, custom_theme = 2),
      "Setting both bw_theme to TRUE and specifying a custom"
    ),
    "custom_theme must be a valid 'theme' object as used in ggplot"
  )

  ## plotly result
  edgeR_res_py <- dispersion_est(seqdata_grp, method = "edgeR", interactive = TRUE)
  deseq2_res_py <- suppressWarnings(dispersion_est(seqdata_grp, method = "DESeq2", interactive = TRUE))
  voom_res_py <- dispersion_est(seqdata_grp, method = "voom", interactive = TRUE)

  res <- purrr::map(list(edgeR_res_py, deseq2_res_py, voom_res_py), function(gg) {
    expect_true(inherits(gg, "plotly"))
  })
})