tests/testthat/test_read_fcs.R

In beadplexr: Analysis of Multiplex Cytometric Bead Assays

test_that("Reading flow data is deprecated", {
 expect_warning(
    read_fcs(.file_name = "file_name")
   )
})
#
# # Preparation -------------------------------------------------------------
# .file_name <- system.file("extdata", "K2-C07-A7.fcs", package = "beadplexr")
# .flow_frame <-flowCore::read.FCS(filename = .file_name, transformation = FALSE)
#
#
# # Boundary events can be removed ------------------------------------------
# test_that("Boundary events can be removed", {
#   expect_s3_class(remove_boundary_events(.flow_frame = .flow_frame, .channels = c("FSC-A", "SSC-A")), "flowFrame")
#   expect_s3_class(remove_boundary_events(.flow_frame = .flow_frame, .channels = c("FSC-A")), "flowFrame")
#   # Must have parameters
#   # expect_error(remove_boundary_events(.flow_frame = .flow_frame, .channels = NULL))
# })
#
#
# # Channels can be filtered ------------------------------------------------
# test_that("Channels can be filtered", {
#   expect_s3_class(subset_channels(.flow_frame = .flow_frame, .filter = list("FSC-A" = c(1e5L, 8e5L))), "flowFrame")
#   expect_s3_class(subset_channels(.flow_frame = .flow_frame, .filter = list("FSC-A" = c(-Inf, 8e5L))), "flowFrame")
#   expect_s3_class(subset_channels(.flow_frame = .flow_frame, .filter = NULL), "flowFrame")
#   # Each list element must be a numeric vector of two
#   expect_error(subset_channels(.flow_frame = .flow_frame, .filter = list("FSC-A" = c(8e5L))))
#   expect_error(subset_channels(.flow_frame = .flow_frame, .filter = list("FSC-A" = c("A", "B"))))
# })
#
# # Transformation can be applied -------------------------------------------
# test_that("Transformation can be applied", {
#   expect_s3_class(transform_bead_channels(.flow_frame = .flow_frame, .bead_channels = c("FL6-H", "FL2-H")), "flowFrame")
#   # The channel must exist
#   expect_error(transform_bead_channels(.flow_frame = .flow_frame, .bead_channels = c("FL6-H", "FL23-H")))
#   # Beads are identified by intensity in one channel, and the relative level of the product is given by another channel
#   expect_error(transform_bead_channels(.flow_frame = .flow_frame, .bead_channels = c("FL6-H")))
# })
#
# # Expression set is exportet as data.frame --------------------------------
# test_that("Expression set is exportet as data.frame", {
#   expect_s3_class(as_data_frame_flow_frame(.flow_frame = .flow_frame), "data.frame")
#   expect_s3_class(as_data_frame_flow_frame(.flow_frame = .flow_frame), "tbl")
#   expect_s3_class(as_data_frame_flow_frame(.flow_frame = .flow_frame, .channels = c("FSC-A", "SSC-A")), "tbl")
#   # Parameters must exist
#   expect_error(as_data_frame_flow_frame(.flow_frame = .flow_frame, .channels = c(" ")))
# })
#
#
# # Compensation application ------------------------------------------------
# odd_ff <- .flow_frame
# flowCore::keyword(odd_ff) <- list("SPILL" = flowCore::keyword(odd_ff, "$SPILLOVER")[[1]])
#
# comp_matrix <- diag(1, nrow = 6, ncol = 6)
# colnames(comp_matrix) <- c("FL1-H", "FL2-H", "FL6-H", "FL1-A", "FL2-A", "FL6-A")
#
# test_that("Compensation can be applied", {
#   expect_s3_class(apply_compensation(.flow_frame = .flow_frame, .compensation = NULL), "flowFrame")
#   expect_s3_class(apply_compensation(.flow_frame = .flow_frame, .compensation = "guess"), "flowFrame")
#   expect_s3_class(apply_compensation(.flow_frame = .flow_frame, .compensation = "SPILL"), "flowFrame")
#   expect_s3_class(apply_compensation(.flow_frame = .flow_frame, .compensation = "spillover"), "flowFrame")
#   expect_s3_class(apply_compensation(.flow_frame = .flow_frame, .compensation = comp_matrix), "flowFrame")
#
#   # Warnings
#   expect_warning(apply_compensation(.flow_frame = .flow_frame, .compensation = c("guess", "xxx")))
#   expect_warning(apply_compensation(.flow_frame = .flow_frame, .compensation = "xxx"))
#   expect_warning(apply_compensation(.flow_frame = odd_ff, .compensation = "guess"))
#   expect_warning(apply_compensation(.flow_frame = odd_ff, .compensation = "spill"))
#
#   # Expect error
#   expect_error(apply_compensation(.flow_frame = odd_ff, .compensation = list(list("guess", "XXX"))))
#   expect_error(apply_compensation(.flow_frame = odd_ff, .compensation = data.frame("guess", "XXX")))
# })
# # Clean
# rm(odd_ff, comp_matrix)
#
# # FACS files can be read and processed ------------------------------------
# test_that("FACS files can be read and processed", {
#   expect_s3_class(read_fcs(.file_name = .file_name), "data.frame")
#   expect_s3_class(read_fcs(.file_name = .file_name, .filter = list("FSC-A" =  c(Inf, 5))), "data.frame")
#   expect_s3_class(read_fcs(.file_name = .file_name, .fsc_ssc = c("FSC-H", "SSC-H")), "data.frame")
#   expect_s3_class(read_fcs(.file_name = .file_name, .bead_channels = c("FSC-H", "SSC-H")), "data.frame")
#   # Parameters must exist
#   expect_error(read_fcs(.file_name = .file_name, .fsc_ssc = c("FSC-H", " ")))
#   # Two forward side scatter channels
#   expect_error(read_fcs(.file_name = .file_name, .fsc_ssc = c("FSC-H")))
#   # filter must be list
#   expect_error(read_fcs(.file_name = .file_name, .filter = c("FSC-H")))
# })