tests/testthat/test_deconvolute.R

In BIMSBbioinfo/deconvR: Simulation and Deconvolution of Omic Profiles

library(deconvR)

test_that("deconvolute nnls", {
  data("HumanCellTypeMethAtlas")
  simulation <- simulateCellMix(5, reference = HumanCellTypeMethAtlas)
  bulkTable <- simulation[[1]]
  proportionsTable <- simulation[[2]]

  deconvolution <- deconvolute(
    bulk = bulkTable,
    model = "nnls", reference = HumanCellTypeMethAtlas
  )
  results <- deconvolution[[1]]
  partial_rsq <- deconvolution[[2]]

  vectorlength <- NROW(tidyr::drop_na(merge(bulkTable, HumanCellTypeMethAtlas,
    by = "IDs"
  ))[, -1])

  expect_output(
    deconvolute(bulk = bulkTable, reference = HumanCellTypeMethAtlas),
    message("DECONVOLUTION WITH NNLS")
  )
  expect_output(
    deconvolute(bulk = bulkTable, reference = HumanCellTypeMethAtlas),
    message("SUMMARY OF PARTIAL R-SQUARED VALUES FOR NNLS : ")
  )

  expect_equal(dim(results), c(
    5,
    length(colnames(HumanCellTypeMethAtlas[, -1]))
  ))
  expect_equal(
    dim(deconvolute(
      bulk = bulkTable[-1, ],
      reference = HumanCellTypeMethAtlas
    )[[1]]),
    c(5, length(colnames(HumanCellTypeMethAtlas[, -1])))
  )
  expect_equal(colnames(results), colnames(HumanCellTypeMethAtlas[, -1]))
  expect_equal(lapply(unlist(results[, ]), typeof)[[1]],
    print("double"),
    ignore_attr = TRUE
  )
  expect_equal(sum(results[1, ]), 1)
  expect_equal(sum(results[2, ]), 1)
  expect_equal(sum(results[3, ]), 1)
  expect_equal(sum(results[4, ]), 1)
  expect_equal(sum(results[5, ]), 1)
  expect_error(deconvolute(reference = HumanCellTypeMethAtlas))
  expect_error(deconvolute(
    bulk = bulkTable, model = "n",
    reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(
    bulk = bulkTable, model = "nnls",
    vec = rep_len(1, vectorlength), reference = HumanCellTypeMethAtlas
  ), NA)
  expect_error(deconvolute(
    bulk = bulkTable, model = "nnls",
    vec = rep_len(1, vectorlength - 1),
    reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(
    bulk = bulkTable[, -1], model = "nnls",
    reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(
    model = "nnls",
    reference = HumanCellTypeMethAtlas
  ))
  expect_equal(dim(results), dim(proportionsTable))
  expect_equal(colnames(results), colnames(HumanCellTypeMethAtlas[, -1]))
  expect_equal(rownames(results), rownames(proportionsTable))


  expect_equal(length(partial_rsq), length(simulation[[1]]) - 1)
})

test_that("deconvolute svr", {
  data("HumanCellTypeMethAtlas")
  simulation <- simulateCellMix(5, reference = HumanCellTypeMethAtlas)
  bulkTable <- simulation[[1]]
  proportionsTable <- simulation[[2]]

  deconvolution <- deconvolute(
    bulk = bulkTable, model = "svr",
    reference = HumanCellTypeMethAtlas
  )
  results <- deconvolution[[1]]
  partial_rsq <- deconvolution[[2]]

  vectorlength <- NROW(tidyr::drop_na(merge(bulkTable, HumanCellTypeMethAtlas,
    by = "IDs"
  ))[, -1])

  expect_output(
    deconvolute(
      bulk = bulkTable, model = "svr",
      reference = HumanCellTypeMethAtlas
    ),
    message("DECONVOLUTION WITH SVR")
  )
  expect_output(
    deconvolute(
      bulk = bulkTable, model = "svr",
      reference = HumanCellTypeMethAtlas
    ),
    message("SUMMARY OF PARTIAL R-SQUARED VALUES FOR SVR : ")
  )

  simulation <- simulateCellMix(5, reference = HumanCellTypeMethAtlas)
  bulkTable <- simulation[[1]]
  proportionsTable <- simulation[[2]]
  expect_equal(dim(results), c(
    5,
    length(colnames(HumanCellTypeMethAtlas[, -1]))
  ))
  expect_equal(
    dim(deconvolute(
      bulk = bulkTable[-1, ],
      model = "svr", reference = HumanCellTypeMethAtlas
    )[[1]]),
    c(5, length(colnames(HumanCellTypeMethAtlas[, -1])))
  )
  expect_equal(colnames(results), colnames(HumanCellTypeMethAtlas[, -1]))
  expect_equal(lapply(unlist(results[, ]), typeof)[[1]],
    print("double"),
    ignore_attr = TRUE
  )
  expect_equal(sum(results[2, ]), 1)
  expect_equal(sum(results[3, ]), 1)
  expect_equal(sum(results[4, ]), 1)
  expect_equal(sum(results[5, ]), 1)
  expect_error(deconvolute(
    bulk = bulkTable[, -1], model = "svr",
    reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(
    bulk = bulkTable, model = "svr",
    vec = rep_len(1, vectorlength), reference = HumanCellTypeMethAtlas
  ), NA)
  expect_error(deconvolute(
    bulk = bulkTable, model = "svr",
    vec = rep_len(1, vectorlength - 1),
    reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(
    model = "svr",
    reference = HumanCellTypeMethAtlas
  ))
  expect_equal(dim(results), dim(proportionsTable))
  expect_equal(colnames(results), colnames(HumanCellTypeMethAtlas[, -1]))
  expect_equal(rownames(results), rownames(proportionsTable))

  expect_equal(length(partial_rsq), length(simulation[[1]]) - 1)
})

test_that("deconvolute qp", {
  data("HumanCellTypeMethAtlas")
  simulation <- simulateCellMix(5,
    reference = HumanCellTypeMethAtlas
  )
  bulkTable <- simulation[[1]]
  proportionsTable <- simulation[[2]]

  deconvolution <- deconvolute(
    bulk = bulkTable, model = "qp",
    reference = HumanCellTypeMethAtlas
  )
  results <- deconvolution[[1]]
  partial_rsq <- deconvolution[[2]]

  vectorlength <- NROW(tidyr::drop_na(merge(bulkTable, HumanCellTypeMethAtlas,
    by = "IDs"
  ))[, -1])

  expect_output(
    deconvolute(
      bulk = bulkTable, model = "qp",
      reference = HumanCellTypeMethAtlas
    ),
    message("DECONVOLUTION WITH QP")
  )
  expect_output(
    deconvolute(
      bulk = bulkTable, model = "qp",
      reference = HumanCellTypeMethAtlas
    ),
    message("SUMMARY OF PARTIAL R-SQUARED VALUES FOR QP : ")
  )

  expect_equal(dim(results), c(
    5,
    length(colnames(HumanCellTypeMethAtlas[, -1]))
  ))
  expect_equal(
    dim(deconvolute(
      bulk = bulkTable[-1, ], model = "qp",
      reference = HumanCellTypeMethAtlas
    )[[1]]),
    c(5, length(colnames(HumanCellTypeMethAtlas[, -1])))
  )
  expect_equal(colnames(results), colnames(HumanCellTypeMethAtlas[, -1]))
  expect_equal(lapply(unlist(results[, ]), typeof)[[1]], print("double"),
    ignore_attr = TRUE
  )
  expect_equal(sum(results[1, ]), 1)
  expect_equal(sum(results[2, ]), 1)
  expect_equal(sum(results[3, ]), 1)
  expect_equal(sum(results[4, ]), 1)
  expect_equal(sum(results[5, ]), 1)
  expect_error(deconvolute(
    bulk = bulkTable[, -1], model = "qp",
    reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(
    bulk = bulkTable, model = "qp",
    vec = rep_len(1, vectorlength), reference = HumanCellTypeMethAtlas
  ), NA)
  expect_error(deconvolute(
    bulk = bulkTable, model = "qp",
    vec = rep_len(1, vectorlength - 1), reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(model = "qp", reference = HumanCellTypeMethAtlas))
  expect_equal(dim(results), dim(proportionsTable))
  expect_equal(colnames(results), colnames(HumanCellTypeMethAtlas[, -1]))
  expect_equal(rownames(results), rownames(proportionsTable))

  expect_equal(length(partial_rsq), length(simulation[[1]]) - 1)
})

test_that("deconvolute rlm", {
  data("HumanCellTypeMethAtlas")
  simulation <- simulateCellMix(5, reference = HumanCellTypeMethAtlas)
  bulkTable <- simulation[[1]]
  proportionsTable <- simulation[[2]]

  deconvolution <- deconvolute(
    bulk = bulkTable, model = "rlm",
    reference = HumanCellTypeMethAtlas
  )
  results <- deconvolution[[1]]
  partial_rsq <- deconvolution[[2]]

  vectorlength <- NROW(tidyr::drop_na(merge(bulkTable,
    HumanCellTypeMethAtlas,
    by = "IDs"
  ))[, -1])

  expect_output(
    deconvolute(
      bulk = bulkTable, model = "rlm",
      reference = HumanCellTypeMethAtlas
    ),
    message("DECONVOLUTION WITH RLM", "\n")
  )
  expect_output(
    deconvolute(
      bulk = bulkTable, model = "rlm",
      reference = HumanCellTypeMethAtlas
    ),
    message("SUMMARY OF PARTIAL R-SQUARED VALUES FOR RLM : ")
  )

  expect_equal(dim(results), c(
    5,
    length(colnames(HumanCellTypeMethAtlas[, -1]))
  ))
  expect_equal(
    dim(deconvolute(
      bulk = bulkTable[-1, ], model = "rlm",
      reference = HumanCellTypeMethAtlas
    )[[1]]),
    c(5, length(colnames(HumanCellTypeMethAtlas[, -1])))
  )
  expect_equal(colnames(results), colnames(HumanCellTypeMethAtlas[, -1]))
  expect_equal(lapply(unlist(results[, ]), typeof)[[1]], print("double"),
    ignore_attr = TRUE
  )
  expect_equal(sum(results[1, ]), 1)
  expect_equal(sum(results[2, ]), 1)
  expect_equal(sum(results[3, ]), 1)
  expect_equal(sum(results[4, ]), 1)
  expect_equal(sum(results[5, ]), 1)
  expect_error(deconvolute(
    bulk = bulkTable[, -1], model = "rlm",
    reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(
    bulk = bulkTable, model = "rlm",
    vec = rep_len(1, vectorlength), reference = HumanCellTypeMethAtlas
  ), NA)
  expect_error(deconvolute(
    bulk = bulkTable, model = "rlm",
    vec = rep_len(1, vectorlength - 1), reference = HumanCellTypeMethAtlas
  ))
  expect_error(deconvolute(model = "rlm", reference = HumanCellTypeMethAtlas))
  expect_equal(dim(results), dim(proportionsTable))
  expect_equal(colnames(results), colnames(HumanCellTypeMethAtlas[, -1]))
  expect_equal(rownames(results), rownames(proportionsTable))

  expect_equal(length(partial_rsq), length(simulation[[1]]) - 1)
})