tests/testthat/test_txs_ms_dge.R

In argschwind/dropseqr: Utilities for Drop-seq data processing

context("Calculate species-specific transcripts from mixed species experiments")

test_that("correct output is produced from dge summary data", {

  # create mock dge summary data -----------------------------------------------

  # generate cell barcodes
  cells <- c("TTCTTGAGTGTT", "TGGTGGTCTTGA", "CAAAAACGGGTT", "GCCTTGCAATGC")

  # number of genes and transcripts
  h_genes <- c(4500, 100, 900, 150)
  m_genes <- c(100, 4000, 300, 5)
  h_txs <- h_genes * 5
  m_txs <- m_genes * 5

  # create data.frame containing dge summary
  dge_summary <- data.frame(CELL_BARCODE = cells,
                            NUM_GENES_HUMAN = h_genes,
                            NUM_TRANSCRIPTS_HUMAN = h_txs,
                            NUM_GENES_MOUSE = m_genes,
                            NUM_TRANSCRIPTS_MOUSE = m_txs,
                            stringsAsFactors = FALSE
                            )

  # test with default settings -------------------------------------------------
  expect_out <- data.frame(cell_barcode = cells,
                           num_transcripts_human = h_txs,
                           num_transcripts_mouse = m_txs,
                           frac_transcripts_human = h_txs / (h_txs + m_txs),
                           frac_transcripts_mouse = m_txs / (h_txs + m_txs),
                           species = c("human", "mouse", "mixed", NA),
                           stringsAsFactors = FALSE
                           )

  # run test
  expect_equal(txs_ms_dge_summary(dge_summary), expected = expect_out)

  # adjust min_txs parameter ---------------------------------------------------
  expect_out[4, "species"] <- "human"

  # run test
  expect_equal(txs_ms_dge_summary(dge_summary, min_txs = 500),
               expected = expect_out)

  # adjust min_frac parameter --------------------------------------------------
  expect_out[4, "species"] <- NA  # revert previous change
  expect_out[3, "species"] <- "human"

  # run test
  expect_equal(txs_ms_dge_summary(dge_summary, min_frac = 0.75),
               expected = expect_out)

})

test_that("correct output is produced from dge data", {

  # create mock dge summary data -----------------------------------------------

  # generate gene expression profile for cells
  genex <- data.frame(TTCTTGAGTGTT = c(1300, 5),
                      TGGTGGTCTTGA = c(0, 1000),
                      CAAAAACGGGTT = c(750, 250),
                      GCCTTGCAATGC = c(500, 2)
                      )

  # create data.frame containing dge data
  dge <- data.frame(GENE = paste0("GENE", 1:2),
                    SPECIES = c("human", "mouse"),
                    genex
                    )

  # test with default settings -------------------------------------------------

  # create expected output
  h_txs <- as.numeric(dge[1, -c(1:2)])
  m_txs <- as.numeric(dge[2, -c(1:2)])

  expect_out <- data.frame(cell_barcode = colnames(genex),
                           num_transcripts_human = h_txs,
                           num_transcripts_mouse = m_txs,
                           frac_transcripts_human = h_txs / (h_txs + m_txs),
                           frac_transcripts_mouse = m_txs / (h_txs + m_txs),
                           species = c("human", "mouse", "mixed", NA),
                           stringsAsFactors = FALSE
  )

  # run test
  expect_equal(txs_ms_dge(dge), expected = expect_out)

  # adjust min_txs parameter ---------------------------------------------------
  expect_out[4, "species"] <- "human"

  # run test
  expect_equal(txs_ms_dge(dge, min_txs = 500), expected = expect_out)

  # adjust min_frac parameter --------------------------------------------------
  expect_out[4, "species"] <- NA  # revert previous change
  expect_out[3, "species"] <- "human"

  # run test
  expect_equal(txs_ms_dge(dge, min_frac = 0.75), expected = expect_out)

})