#############################################################
## This set implements additional compliance tests that
## were not included with Gating-ML 2.0. We have used R to
## generate the expected results and therefore, these tests
## are more just a sanity check whether the results are
## consistent. Also, here, we are checking a few concepts
## that are not checked with the official tests.
#############################################################
fcsFile <- system.file("extdata/Gml2/FCSFiles", "9399_1_3_NKR.fcs", package = "gatingMLData")
gateFile <- system.file("extdata/Gml2/Gating-MLFiles","gates3.xml", package = "gatingMLData")
csvFile <- system.file("extdata/Gml2/ExpectedResults/set_3", package = "gatingMLData")
flowEnv=new.env()
read.gatingML(gateFile, flowEnv)
fcs <- read.FCS(fcsFile, transformation="linearize-with-PnG-scaling")
test.my3DRectangleGate <- function()
{
gateId <- "my3DRectangleGate"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myBooleanAnd <- function()
{
gateId <- "myBooleanAnd"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myBooleanNot <- function()
{
gateId <- "myBooleanNot"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myBooleanOr <- function()
{
gateId <- "myBooleanOr"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myBooleanOrWithParent <- function()
{
gateId <- "myBooleanOrWithParent"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myEllipseGate <- function()
{
gateId <- "myEllipseGate"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myEllipsoidGate <- function()
{
gateId <- "myEllipsoidGate"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGate <- function()
{
gateId <- "myPolygonGate"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGate2ArcSinHLin <- function()
{
gateId <- "myPolygonGate2ArcSinHLin"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGate3LogLin <- function()
{
gateId <- "myPolygonGate3LogLin"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithCustomInvertedAlreadySpillover <- function()
{
gateId <- "myPolygonGateWithCustomInvertedAlreadySpillover"
# csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", "myPolygonWithCustInvAlrSpil", ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithCustomNonSquareSpectrumMatrix <- function()
{
gateId <- "myPolygonGateWithCustomNonSquareSpectrumMatrix"
# csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", "myPolygonWithCustNonSqSpecMat", ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithCustomNonSquareSpectrumMatrixInvertedAlready <- function()
{
gateId <- "myPolygonGateWithCustomNonSquareSpectrumMatrixInvertedAlready"
# csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", "myPolygonWCustNonSqSpecInvAlrd", ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithCustomNonSquareSpectrumMatrixOnArcSinH <- function()
{
gateId <- "myPolygonGateWithCustomNonSquareSpectrumMatrixOnArcSinH"
# csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", "myPolygonWCustNonSqSpecArcSinH", ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithCustomSpillover <- function()
{
gateId <- "myPolygonGateWithCustomSpillover"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithCustomSpilloverAndArcSinH <- function()
{
gateId <- "myPolygonGateWithCustomSpilloverAndArcSinH"
# csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", "myPolygonWCustSpillAndArcSinH", ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithFCSSpillover <- function()
{
gateId <- "myPolygonGateWithFCSSpillover"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithFCSSpilloverAndArcSinH <- function()
{
gateId <- "myPolygonGateWithFCSSpilloverAndArcSinH"
# csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", "myPolygonWFCSSpillAndArcSinH", ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithoutSpillover <- function()
{
gateId <- "myPolygonGateWithoutSpillover"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myPolygonGateWithSpilloverSameAsFCS <- function()
{
gateId <- "myPolygonGateWithSpilloverSameAsFCS"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRangeGate1 <- function()
{
gateId <- "myRangeGate1"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRangeGate2 <- function()
{
gateId <- "myRangeGate2"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRectangleGate <- function()
{
gateId <- "myRectangleGate"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRectangleGate2bHyperlog <- function()
{
gateId <- "myRectangleGate2bHyperlog"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRectangleGate2Logicle <- function()
{
gateId <- "myRectangleGate2Logicle"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRectangleGate3bHyperlogArcSinH <- function()
{
gateId <- "myRectangleGate3bHyperlogArcSinH"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRectangleGate3LogicleArcSinH <- function()
{
gateId <- "myRectangleGate3LogicleArcSinH"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRectangleGate4bHyperlogArcSinHFCSCompensated <- function()
{
gateId <- "myRectangleGate4bHyperlogArcSinHFCSCompensated"
# csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", "myRect4bHyperlogArcSinHFCSComp", ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.myRectangleGate4LogicleArcSinHFCSCompensated <- function()
{
gateId <- "myRectangleGate4LogicleArcSinHFCSCompensated"
# csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", "myRect4LogicleArcSinHFCSComp", ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q1 <- function()
{
gateId <- "Q1"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q1A <- function()
{
gateId <- "Q1A"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q1B <- function()
{
gateId <- "Q1B"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q1C <- function()
{
gateId <- "Q1C"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q1D <- function()
{
gateId <- "Q1D"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q1E <- function()
{
gateId <- "Q1E"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q2 <- function()
{
gateId <- "Q2"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q2A <- function()
{
gateId <- "Q2A"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q2B <- function()
{
gateId <- "Q2B"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q2C <- function()
{
gateId <- "Q2C"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q2D <- function()
{
gateId <- "Q2D"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q2E <- function()
{
gateId <- "Q2E"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q3 <- function()
{
gateId <- "Q3"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q3A <- function()
{
gateId <- "Q3A"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q3B <- function()
{
gateId <- "Q3B"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q3C <- function()
{
gateId <- "Q3C"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q3D <- function()
{
gateId <- "Q3D"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q3E <- function()
{
gateId <- "Q3E"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q4 <- function()
{
gateId <- "Q4"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q4A <- function()
{
gateId <- "Q4A"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q4B <- function()
{
gateId <- "Q4B"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q4C <- function()
{
gateId <- "Q4C"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q4D <- function()
{
gateId <- "Q4D"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q4E <- function()
{
gateId <- "Q4E"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q5 <- function()
{
gateId <- "Q5"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q6 <- function()
{
gateId <- "Q6"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
test.Q7 <- function()
{
gateId <- "Q7"
csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
expectedResult <- read.csv(csvFile, header = FALSE)
flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}
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