tests/testthat/test_data.R

In jasonserviss/CIMseq: CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

context("CIMseqData")

test_that("check that the CIMseqSinglets function outputs the expected result", {
  expect_silent(CIMseqSinglets(
    getData(CIMseqSinglets_test, "counts"),
    getData(CIMseqSinglets_test, "counts.ercc"),
    getData(CIMseqSinglets_test, "dim.red"),
    getData(CIMseqSinglets_test, "classification")
  ))
})

test_that("check that the CIMseqMultiplets function outputs the expected result", {
  expect_silent(CIMseqMultiplets(
    getData(CIMseqMultiplets_test, "counts"),
    getData(CIMseqMultiplets_test, "counts.ercc"),
    getData(CIMseqMultiplets_test, "features")
  ))
})

test_that("check that the .norm.counts function outputs the expected result", {
    
  ###TEST1####
  #prepare normal input data
  input <- matrix(c(0,1,1,0), nrow = 2, ncol = 2)
  
  #setup expected data
  expected <- matrix(
    c(0, 1000000, 1000000, 0),
    nrow = 2,
    ncol = 2
  )
  
  #run function
  output <- .norm.counts(input)
  
  #test
  expect_true(all.equal(expected, output))
})

test_that("check that the .norm.log.counts function outputs the expected result", {
  c <- getData(CIMseqSinglets_test, "counts")
  expect_true(all.equal(.norm.log.counts(c), log2(.norm.counts(c) + 1)))
})

test_that("check that the .inputCheckSinglets outputs the expected result", {
    
    ###TEST1####
    #non-conforming counts and counts.ercc
    #setup input
    counts <- matrix(1:10, ncol = 10)
    counts.ercc <- matrix(1:11, ncol = 11)
    classification <- rep("A", 10)
    dim.red <- matrix(1:20, nrow = 10)
    
    #test
    expect_message(
      .inputCheckSinglets(
        counts, counts.ercc, dim.red, classification
      )
    )
    
    ###TEST2####
    #NA's present
    #setup input
    counts <- matrix(NA, ncol = 10)
    counts.ercc <- matrix(NA, ncol = 11)
    
    #test
    expect_message(
      .inputCheckSinglets(
        counts, counts.ercc, dim.red, classification
      )
    )
    
    ###TEST3####
    #classification too few
    expect_message(
      .inputCheckSinglets(
        counts, counts.ercc, dim.red, classification[1:2]
      )
    )
    
    ###TEST4####
    #dim.red too few
    expect_message(
      .inputCheckSinglets(
        counts, counts.ercc, dim.red[1:5, ], classification
      )
    )
})

test_that("check that the .inputCheckMultiplets outputs the expected result", {
  
  ###TEST1####
  #non-conforming counts and counts.ercc
  #setup input
  counts <- matrix(1:10, ncol = 10)
  counts.ercc <- matrix(1:11, ncol = 11)
  classification <- rep("A", 10)
  dim.red <- matrix(1:20, nrow = 10)
  
  #test
  expect_message(.inputCheckMultiplets(counts, counts.ercc))
  
  ###TEST2####
  #NA's present
  #setup input
  counts <- matrix(NA, ncol = 10)
  counts.ercc <- matrix(NA, ncol = 11)
  
  #test
  expect_message(.inputCheckMultiplets(counts, counts.ercc))
})

test_that("check that estimateCells outputs the expected result", {
    
  ###TEST1####
  #setup expected data
  expected1 <- tibble::tibble(
    sampleType=c(rep("Singlet", 79), rep("Multiplet", 3))
  )
  
  expected2 <- tibble::tibble(
    frac.ercc = 0,
    estimatedCellNumber = 1
  )
  
  expected3 <- tibble::tibble(
    frac.ercc = 0,
    estimatedCellNumber = 2
  )
  
  #run function
  output <- estimateCells(CIMseqSinglets_test, CIMseqMultiplets_test)
  firstRow <- output %>%
    dplyr::slice(1) %>%
    dplyr::select(frac.ercc:estimatedCellNumber) %>%
    round()
  lastRow <- output %>%
    dplyr::slice(nrow(output)) %>%
    dplyr::select(frac.ercc:estimatedCellNumber) %>%
    round()
  
  #test
  expect_identical(expected1, dplyr::select(output, `sampleType`))
  expect_identical(expected2, firstRow)
  expect_identical(expected3, lastRow)
  expect_type(output$sample, "character")
  expect_type(output$sampleType, "character")
  expect_type(output$frac.ercc, "double")
  expect_type(output$estimatedCellNumber, "double")
})

test_that("check that estimateCells gives error with all 0 ercc", {
  ercc <- getData(CIMseqSinglets_test, "counts.ercc")
  ercc[ ,1] <- rep(0, nrow(ercc))
  tmp <- CIMseqSinglets_test
  getData(tmp, "counts.ercc") <- ercc
  expect_warning(estimateCells(tmp, CIMseqMultiplets_test))
  
  ercc[ ,2:6] <- rep(0, nrow(ercc) * 5)
  getData(tmp, "counts.ercc") <- ercc
  expect_warning(estimateCells(tmp, CIMseqMultiplets_test))
})

test_that("estimateCells correct with theoretical.max argument non-null", {
  theoretical.max <- 2
  output <- estimateCells(
    CIMseqSinglets_test, CIMseqMultiplets_test, 
    theoretical.max = theoretical.max
  )
  expect_true(max(pull(output, estimatedCellNumber)) <= theoretical.max)
})