tests/testthat/test-cyto_spillover_compute.R

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

context("cyto_spillover_compute")

# CYTO_SPILLOVER_COMPUTE -------------------------------------------------------

# UNIVERSAL UNSTAINED CONTROL
test_that("cyto_spillover_compute universal reference", {
  
  # GATES
  mock_locator <- mock(list("x" = 1740,
                            "y" = 50),
                       list("x" = 4265,
                            "y" = 50),
                       list("x" = 1800,
                            "y" = 50),
                       list("x" = 3100,
                            "y" = 50),
                       list("x" = 1710,
                            "y" = 50),
                       list("x" = 2950,
                            "y" = 50),
                       list("x" = 2720,
                            "y" = 50),
                       list("x" = 4115,
                            "y" = 50),
                       list("x" = 2310,
                            "y" = 50),
                       list("x" = 3780,
                           "y" = 50),
                       list("x" = 2350,
                            "y" = 50),
                       list("x" = 4120,
                            "y" = 50),
                       cycle = TRUE)
  
  # SPILL
  SPILL <- read.csv("Reference-Universal-Spillover-Matrix.csv",
                    header = TRUE,
                    row.names = 1,
                    stringsAsFactors = FALSE)
  SPILL <- as.matrix(SPILL)
  colnames(SPILL) <- cyto_fluor_channels(gs_comp)
  rownames(SPILL) <- cyto_fluor_channels(gs_comp)
  
  # GATINGSET
  testthat::with_mock(locator = mock_locator,{
                        expect_equal(
                          cyto_spillover_compute(gs_comp,
                                                 parent = "Single Cells",
                                                 channel_match = "Reference-Compensation-Channels.csv",
                                                 spillover = "Spillover-Matrix.csv"),
                          SPILL)
                      })

  expect_true(file.exists("Spillover-Matrix.csv"))
  
  # SAVED MATRIX
  spill <- read.csv("Spillover-Matrix.csv",
                    header = TRUE,
                    row.names = 1,
                    stringsAsFactors = FALSE)
  colnames(spill) <- rownames(spill)
  spill <- as.matrix(spill)
  expect_equal(spill, SPILL)
  
})

# INTERNAL UNSTAINED REFERENCE
test_that("cyto_spillover_compute internal reference", {

  # CHANNELS
  mock_data_editor <- mock(data.frame("name" = cyto_names(gs_comp[-length(gs_comp)]),
                                      "channel" = c("7-AAD-A",
                                                    "Alexa Fluor 700-A",
                                                    "APC-Cy7-A",
                                                    "Alexa Fluor 647-A",
                                                    "Alexa Fluor 488-A",
                                                    "PE-A"),
                                      stringsAsFactors = FALSE))

  # GATES
  mock_locator <- mock(list("x" = -0.109,
                            "y" = 50),
                       list("x" = 1.234,
                            "y" = 50),
                       list("x" = 1.927,
                            "y" = 50),
                       list("x" = 3.685,
                            "y" = 50),
                       list("x" = -0.204,
                            "y" = 50),
                       list("x" = 1.637,
                            "y" = 50),
                       list("x" = 2.012,
                            "y" = 50),
                       list("x" = 4.003,
                            "y" = 50),
                       list("x" = -0.126,
                            "y" = 50),
                       list("x" = 1.465,
                            "y" = 50),
                       list("x" = 1.83,
                            "y" = 50),
                       list("x" = 3.808,
                            "y" = 50),
                       list("x" = -0.838,
                            "y" = 50),
                       list("x" = 1.39,
                            "y" = 50),
                       list("x" = 2.602,
                            "y" = 50),
                       list("x" = 4.622,
                            "y" = 50),
                       list("x" = 0.306,
                            "y" = 50),
                       list("x" = 1.702,
                            "y" = 50),
                       list("x" = 2.587,
                            "y" = 50),
                       list("x" = 4.421,
                            "y" = 50),
                       list("x" = 0.435,
                            "y" = 50),
                       list("x" = 2.14,
                            "y" = 50),
                       list("x" = 2.891,
                            "y" = 50),
                       list("x" = 4.305,
                            "y" = 50),
                       cycle = TRUE)

  # SPILL
  SPILL <- read.csv("Reference-Internal-Spillover-Matrix.csv",
                    header = TRUE,
                    row.names = 1,
                    stringsAsFactors = FALSE)
  SPILL <- as.matrix(SPILL)
  colnames(SPILL) <- cyto_fluor_channels(gs_comp)
  rownames(SPILL) <- cyto_fluor_channels(gs_comp)

  # TRANSFORMED GATINGSET
  testthat::with_mock(data_editor = mock_data_editor,
                      locator = mock_locator, {
                        expect_equal(
                          cyto_spillover_compute(gs_comp_trans[seq_len(length(gs_comp)-1)],
                                                 parent = "Single Cells",
                                                 spillover = "Spillover-Matrix.csv"),
                          SPILL)
                      })

  expect_true(file.exists("Spillover-Matrix.csv"))

  # SAVED MATRIX
  spill <- read.csv("Spillover-Matrix.csv",
                    header = TRUE,
                    row.names = 1,
                    stringsAsFactors = FALSE)
  colnames(spill) <- rownames(spill)
  spill <- as.matrix(spill)
  expect_equal(spill, SPILL)

})

# DELETE FILES
base::unlink("Spillover-Matrix.csv")
base::unlink(paste0(format(Sys.Date(), "%d%m%y"),"-Compensation-Channels.csv"))