suppressPackageStartupMessages({
library(flowCore)
library(SingleCellExperiment)
})
data(GvHD)
fs <- GvHD[seq_len(5)]
sce <- prepData(fs[[1]])
test_that(".read_fs() - input arguments", {
u <- fs
class(u) <- "x"
expect_error(.read_fs(u))
u <- flowSet_to_list(fs)
u[[1]] <- "x"
expect_error(.read_fs(u))
u <- system.file("extdata", package = "flowCore")
u <- file.path(u, dir(u))[seq_len(3)]
u[1] <- "x"
expect_error(.read_fs(u))
})
test_that(".read_fs() - 'flowSet' as input", {
x <- .read_fs(fs)[[1]]
expect_identical(x, fs)
})
test_that(".read_fs() - 'flowFrame's as input", {
ffs <- list(fs[[1]], fs[[2]])
x <- .read_fs(ffs)[[1]]
expect_equal(x, flowSet(ffs))
})
test_that(".read_fs() - FCS files as input", {
fcs <- system.file("extdata", package = "flowCore")
fcs <- file.path(fcs, dir(fcs))[seq_len(3)]
x <- .read_fs(fcs)[[1]]
y <- lapply(fcs, read.FCS,
transformation = FALSE,
truncate_max_range = FALSE)
expect_is(x, "flowSet")
expect_equal(x, flowSet(y))
})
# ------------------------------------------------------------------------------
test_that(".transform() - input arguments", {
cfs <- seq_len(nrow(sce))
names(cfs) <- channels(sce)
cfs1 <- unname(cfs)
cfs2 <- cfs
names(cfs2)[1] <- "x"
for (cf in list(0, "x", cfs1, cfs2))
expect_error(.transform(sce, cf))
})
test_that(".transform() - single cofactor", {
cf <- sample(10, 1)
cfs <- rep(cf, nrow(sce))
names(cfs) <- channels(sce)
x <- .transform(sce, cf)
y <- .transform(sce, cfs)
int_metadata(x)$cofactor <- NULL
int_metadata(y)$cofactor <- NULL
expect_identical(x, y)
})
test_that(".transform() - channel-specific cofactors", {
cfs <- seq_len(nrow(sce))
names(cfs) <- channels(sce)
expect_identical(
.transform(sce, cfs),
.transform(sce, sample(cfs)))
})
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