context("2d clustering")
flowDataPath <- system.file("extdata", package = "flowWorkspaceData")
fcsFiles <- list.files(pattern = "CytoTrol", flowDataPath, full = TRUE)
fs <- read.flowSet(fcsFiles)
Sys.setenv("_R_CHECK_LIMIT_CORES_" = "warn")
# test_that("construct ellipse from prior", {
# set.seed(1)
# require(openCyto)
# chnl <- c("FSC-A","SSC-A")
# prior <- prior_flowclust(fs ,chnl, K = 2)
# colnames(prior$Mu0) <- chnl
# cov <- prior$Lambda0[1,,]/(prior$nu0[1]-2-1)
# mu <- prior$Mu0[1,]
#
# mat1 <- ellipse::ellipse(cov,centre=mu, npoints = 50)
#
# mat2 <- ellipse(cov,centre=mu)
# expect_equivalent(mat1, mat2)
# plot(exprs(fs[[1]])[,chnl], pch = ".")
# lines(mat1, col = "green", lty = "dotted")
# lines(mat2, col = "red", , lty = "dashed")
# plotPrior(fs[[1]], prior)
# })
test_that("flowClust 2d: prior", {
skip("to temporarily bypass bioc check error for windows and aarch64 linux")
RNGversion("3.5")#quick fix to pass the test against the results that were previously generated from older R (<=2018/11/06)
set.seed(1)
require(openCyto)
prior <- prior_flowclust(fs ,c("FSC-A", "SSC-A"), K = 2)
options("mc.cores" = 1)
g <-
gate_flowclust_2d(
fs[[1]],
"FSC-A",
"SSC-A",
K = 2,
target = c(1e5, 5e4),
prior = prior,
usePrior = "yes"
)
expect_equal(g@cov, structure(c(1173858741, 523766402, 523766402, 625519945)
, .Dim = c(2L, 2L)
, .Dimnames = list(c("FSC-A", "SSC-A"), c("FSC-A", "SSC-A")))
, tolerance = 1e-6
)
expect_equal(g@distance, 2.94, tolerance =1e-3)
expect_equal(g@mean, c("FSC-A" = 87638, "SSC-A" = 62425), tolerance = 1e-5)
})
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