tests/testthat/test_count_touching_cells.R

In akoyabio/phenoptr: inForm Helper Functions

library(testthat)

test_that('count_touching_cells works', {
  cell_seg_path =
    test_path('test_data',
              'FIHC4__0929309_HP_IM3_2_cell_seg_data.txt')

  pairs = list(c("Helper T", "B"),
               c("Helper T", "Cytotoxic T"),
               c("Helper T", "Helper T"),
               c("Helper T", "FOO+"))

  # Colors for all the phenotypes mentioned in pairs
  colors = list(
    'Cytotoxic T' = 'yellow',
    'Helper T' = 'green',
    'B' = 'red',
    'FOO+' = 'pink'
  )

  output_base = tempdir()

  # Error checking
  # These get an error *and* a warning
  expect_warning(
    expect_error(count_touching_cells(cell_seg_path, pairs, write_images=TRUE),
                 'requires colors'),
    'Omitting')

  expect_warning(
    expect_error(count_touching_cells(cell_seg_path, pairs,
                                    colors=list('CD8+' = 'yellow')),
               'requires colors'),
    'Omitting')

  # This one works with multiple warnings
  warnings = capture_warnings(
    counts <- count_touching_cells(cell_seg_path, pairs, colors,
                                   categories='Tumor',
                                   output_base=output_base))

  expect_match(warnings[1], 'Omitting Helper T - Helper T')
  expect_match(warnings[2], 'Helper T touching FOO+')
  expect_equal(dim(counts), c(3, 9))
  expect_equal(counts$phenotype1, rep('Helper T', 3))
  expect_equal(counts$phenotype2, c('B', 'Cytotoxic T', 'FOO+'))
  expect_equal(counts$total1, rep(15, 3))
  expect_equal(counts$total2, c(249, 6, 0))
  expect_equal(counts$p1_touch_p2, c(14, 3, 0))
  expect_equal(counts$p2_touch_p1, c(23, 4, 0))
  expect_equal(counts$touch_pairs, c(31, 5, 0))

  image_names = list.files(output_base, '_touch_')
  expect_equal(length(image_names), 2)

  # Don't do the image compare on Travis, it fails...
  # There are minor differences in the actual image on macOS, hence
  # the tolerance. We are just looking for diffs in the saturated colors
  # representing the cells of interest.
  if (!identical(Sys.getenv("TRAVIS"), "true")) {
    test_base = test_path('test_results')
    for (image_name in image_names) {
      # Read the result images and compare to a reference
      actual = tiff::readTIFF(file.path(output_base, image_name), as.is=TRUE)
      expected = tiff::readTIFF(file.path(test_base, image_name), as.is=TRUE)
      expect_equal(actual, expected, tolerance=0.1, info=image_name)
    }
  }
})

test_that('count_touching_cells_fast works', {
  cell_seg_path =
    file.path('C:/Research/phenoptrTestData/touching_cells',
              '180628 B-lung2_Scan1_[14659,46741]_cell_seg_data.txt')
  skip_if_not(file.exists(cell_seg_path))

  csd = read_cell_seg_data(cell_seg_path)
  field_name = "180628 B-lung2_Scan1_[14659,46741]"
  export_path = dirname(cell_seg_path)
  phenos = list("CD8+", "CD68+")
  color1 = 'cyan'
  color2 = 'red'

  result = count_touching_cells_fast(csd, field_name, export_path,
                                       phenos, color1, color2)

  expected_path = file.path(export_path,
                      '180628 B-lung2_Scan1_[14659,46741]_CD8+_touch_CD68+.tif')
  expected = EBImage::readImage(expected_path)

  expect_equal(result$image, expected)
  expect_equal(dim(result$data), c(49, 12))

  # Test error checking for non-distinct phenotypes.
  # This is egregious duplication.
  phenos = list("CD8+", "CD8+")
  expect_error(count_touching_cells_fast(csd, field_name, export_path,
                            phenos, color1, color2),
               'Found 688 cells')
})

test_that('replace_invalid_path_characters works', {
  bad = "<>:\"/\\|?* "

  expect_equal(replace_invalid_path_characters(bad, "_"), "__________")

  bad = paste0("a", bad, "b")
  expect_equal(replace_invalid_path_characters(bad, "_"), "a__________b")

  bad = "a<b>c:d\"e/f\\g|h?i*j k"
  expect_equal(replace_invalid_path_characters(bad, "_"),
    "a_b_c_d_e_f_g_h_i_j_k")

  # Replacement can be multiple chars
  expect_equal(replace_invalid_path_characters(bad, "_="),
    "a_=b_=c_=d_=e_=f_=g_=h_=i_=j_=k")

  # or nothing
  expect_equal(replace_invalid_path_characters(bad, ""), "abcdefghijk")

  # Replacement can't contain invalid characters
  expect_error(replace_invalid_path_characters(bad, "*"), 'invalid')
})