tests/testthat/testCreateDistributionPlot.R

In PhyloProfile: PhyloProfile

context("test creating data and plots for distritbution analysis function")

test_that("test distritbution analyze functions", {
    # raw input
    inputData <- createLongMatrix("mainWideTest.txt")
    # selected rank name
    rankName <- "species"
    # distribution data for percentage of species present in supertaxa
    percentDistributionData <- createPercentageDistributionData(
        inputData, rankName
    )
    expect_true(nrow(percentDistributionData) == 18)

    # distribution data for 2 additional variables
    distributionData <- createVariableDistributionData(
        inputData, c(0, 1), c(0.5, 1)
    )
    expect_true(nrow(distributionData) == 17)

    # distribution data for 2 additional variables of a subset of taxa
    inputTaxonID <- getInputTaxaID(inputData)
    inputTaxonName <- getInputTaxaName(rankName, inputTaxonID)
    refTaxon <- inputTaxonName$fullName[1]
    taxaTree <- NULL
    sortedTaxa <- sortInputTaxa(
        inputTaxonID, rankName, refTaxon, taxaTree
    )
    taxaCount <- plyr::count(sortedTaxa, "supertaxon")
    fullProfileData <- parseInfoProfile(
        inputData,
        sortedTaxa,
        taxaCount,
        999
    )
    selectedGenes <- c("100136at6656", "103479at6656")
    selectedTaxa <- c("Homo sapiens", "Branchiostoma floridae")
    subsetDistributionData <- createVariableDistributionDataSubset(
        fullProfileData,
        distributionData,
        selectedGenes,
        selectedTaxa
    )
    expect_true(ncol(subsetDistributionData) == 5)

    # plot distribution of var1
    p <- createVarDistPlot(
        distributionData, "variable 1 name", "var1", NULL, 12
    )
    expect_true(nrow(p$data) == 17)
})