tests/testthat/test_phenotype.R

In maize-genetics/rTASSEL: R Front-End for TASSEL

# === Tests for phenotype functions =================================

## Preamble - load data ----

### Start logging info
startLogger()
library(rJava)

### Load hapmap data
genoPathHMP <- system.file(
    "extdata",
    "mdp_genotype.hmp.txt",
    package = "rTASSEL"
)

### Read data - need only non missing data!
phenoPathFast <- system.file(
    "extdata",
    "mdp_traits_nomissing.txt",
    package = "rTASSEL"
)

### Create rTASSEL phenotype only object
tasPheno <- readPhenotypeFromPath(
    path = phenoPathFast
)

### Create rTASSEL genotype only object
tasGeno <- readGenotypeTableFromPath(
    path = genoPathHMP
)

### Create rTASSEL object - use prior TASSEL genotype object
tasGenoPheno <- readGenotypePhenotype(
    genoPathOrObj = genoPathHMP,
    phenoPathDFOrObj = phenoPathFast
)



## Error tests ----
test_that("readPhenotypeFromPath() throws general exceptions.", {
    badPath <- "does/not/exist"
    message <- paste0("Cannot open file ", badPath, ": No such file or directory")

    expect_error(
        object = readPhenotypeFromPath(badPath),
        regexp = message
    )
})

test_that("readPhenotypeFromDataFrame() throws general exceptions.", {

    phenoDF <- getPhenotypeDF(tasGenoPheno)
    phenoDF <- as.data.frame(phenoDF)

    errorMsg <- paste0(
        "Parameter `attributeTypes` contains incorrect attributes.\n",
        "Please select from the following:\n",
        "  taxa\n",
        "  factor\n",
        "  data\n",
        "  covariate\n"
    )

    expect_error(
        object = readPhenotypeFromDataFrame(
            phenotypeDF    = phenoDF,
            taxaID         = "Taxa",
            attributeTypes = "wrong"
        ),
        regexp = errorMsg
    )
})

test_that("getPhenotypeDF() throws general exceptions.", {
    expect_error(
        object = getPhenotypeDF(mtcars),
        regexp = "`tasObj` must be of class `TasselGenotypePhenotype`"
    )
    expect_error(
        object = getPhenotypeDF(tasGeno),
        regexp = "TASSEL phenotype object not found"
    )
})



## Return tests ----
test_that("readPhenotypeFromDataFrame() returns correct data.", {

    phenoDF <- getPhenotypeDF(tasGenoPheno)
    phenoDF <- as.data.frame(phenoDF)

    phenoDFTas <- readPhenotypeFromDataFrame(
        phenotypeDF = phenoDF,
        taxaID = "Taxa"
    )

    expect_true(class(phenoDFTas) == "TasselGenotypePhenotype")
})

test_that("getPhenotypeDF () returns correct data.", {

    phenoDF <- getPhenotypeDF(tasGenoPheno)

    expect_true(class(phenoDF) == "data.frame")

    expect_equal(
        object   = names(phenoDF),
        expected = c("Taxa", "EarHT", "dpoll", "EarDia")
    )
})