tests/testthat/test_transformations.R

In microbiome/microbiome: Microbiome Analytics

context("phyloseq transformations")

test_that("transform works correctly", {
  # Hellinger distance is sqrt of the relative abundance
  # Note the different scales (100x) of these two measures.
  
  data(dietswap)
  
  hel <- otu_table(transform(dietswap, "hellinger"))^2
  rel <- otu_table(transform(dietswap, "compositional"))
  expect_equal(max(abs(hel - rel)), 0, tolerance = 1e-15)

  expect_equal(ntaxa(transform(dietswap, "identity")), ntaxa(dietswap))

  z <- transform(transform(dietswap, "shift", shift = 1), "Z")
  expect_equal(ntaxa(z), ntaxa(dietswap))
  expect_equal(sum(apply(abundances(z), 1, mean)), 0, tolerance = 1e-10)

  # Test also with taxa are cols
  pseq <- dietswap
  dietswap_transpose <- otu_table(t(as.matrix(abundances(pseq))), taxa_are_rows = FALSE)

  # z <- transform(dietswap, "Z", target = "OTU")
  expect_equal(max(abs(rowMeans(abundances(z)))), 0, tolerance = 1e-10)
  expect_true(all(dim(z) == dim(dietswap)))

  z <- transform(dietswap_transpose, "Z", target = "OTU")
  expect_equal(min(abs(rowMeans(abundances(z)))), 0, tolerance = 1e-10)
  expect_true(all(dim(z) == dim(dietswap_transpose)))


  z <- transform(dietswap, "Z", target = "sample")
  expect_equal(max(abs(colMeans(abundances(z)))), 0, tolerance = 1e-10)
  expect_true(all(dim(z) == dim(dietswap)))

  z <- transform(dietswap_transpose, "Z", target = "sample")
  expect_equal(min(abs(colMeans(abundances(z)))), 0, tolerance = 1e-10)
  expect_true(all(dim(z) == dim(dietswap_transpose)))


  expect_equal(ntaxa(transform(dietswap, "clr")), ntaxa(dietswap))
  expect_equal(ntaxa(transform(transform(dietswap, "shift", shift = 1), "log10")), ntaxa(dietswap))
  expect_true(all(transform(abundances(transform(dietswap, "shift", shift = 1))[1:3, 1:3], "log10") == transform(abundances(dietswap)[1:3, 1:3], "log10p")))    

  expect_equal(ntaxa(transform(dietswap, "shift", shift = 1)), ntaxa(dietswap))      
  expect_equal(ntaxa(transform(dietswap, "compositional")), ntaxa(dietswap))
  expect_true(sum(colSums(abundances(transform(dietswap, "compositional"))) - 1) < 1e-15)

  expect_equal(sum(abundances(transform(dietswap, "alr", shift=1, reference=1)) - as.matrix(compositions::alr(abundances(dietswap)+1, ivar=1))), 0, tolerance=1e-6)

})