inst/RUnitGml2Script_Files/runit.04.set4.R

In flowUtils: Utilities for flow cytometry

#############################################################
## 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","gates4.xml", package = "gatingMLData")
csvFile <-  system.file("extdata/Gml2/ExpectedResults/set_4", package = "gatingMLData")

flowEnv=new.env()
read.gatingML(gateFile, flowEnv)
fcs <- read.FCS(fcsFile, transformation="linearize-with-PnG-scaling")

test.myQuadrant_NN <- function()
{
    gateId  <- "myQuadrant_NN"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant_NP <- function()
{
    gateId  <- "myQuadrant_NP"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant_PN <- function()
{
    gateId  <- "myQuadrant_PN"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant_PP <- function()
{
    gateId  <- "myQuadrant_PP"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant2_NN <- function()
{
    gateId  <- "myQuadrant2_NN"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant2_NP <- function()
{
    gateId  <- "myQuadrant2_NP"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant2_PN <- function()
{
    gateId  <- "myQuadrant2_PN"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant2_PP <- function()
{
    gateId  <- "myQuadrant2_PP"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant3_NN <- function()
{
    gateId  <- "myQuadrant3_NN"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant3_NP <- function()
{
    gateId  <- "myQuadrant3_NP"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant3_PN <- function()
{
    gateId  <- "myQuadrant3_PN"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant3_PP <- function()
{
    gateId  <- "myQuadrant3_PP"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant4_NN <- function()
{
    gateId  <- "myQuadrant4_NN"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant4_NP <- function()
{
    gateId  <- "myQuadrant4_NP"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant4_PN <- function()
{
    gateId  <- "myQuadrant4_PN"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myQuadrant4_PP <- function()
{
    gateId  <- "myQuadrant4_PP"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myRange1 <- function()
{
    gateId  <- "myRange1"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myRange2 <- function()
{
    gateId  <- "myRange2"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myRange3 <- function()
{
    gateId  <- "myRange3"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myRange4 <- function()
{
    gateId  <- "myRange4"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}

test.myRange5 <- function()
{
    gateId  <- "myRange5"
    csvFile <- paste(csvFile, .Platform$file.sep, "Results_", gateId, ".txt", sep="")
    expectedResult <- read.csv(csvFile, header = FALSE)
    flowUtils:::performGateTest(gateId, fcs, expectedResult, flowEnv)
}