context("Full data processing pipeline until main plot")
input <- defaultInput()
path <- system.file("extdata/exampleDatabase.db", package = "ShinyLipids")
databaseConnection <- DBI::dbConnect(RSQLite::SQLite(), path)
test_that("Example database exists", {
DBI::dbListTables(databaseConnection) %>%
expect_length(2)
})
test_that("collectLipidClassOrder default return value exists", {
collectLipidClassOrder(databaseConnection) %>%
expect_length(48)
})
test_that("Example meta data exists", {
metaData <- collectMetaData(databaseConnection)
expect_equal(metaData$sample_from[[1]], "Harry Potter")
})
test_that("Example meta data exists", {
rawData <- collectRawData(con = databaseConnection, id = 1)
expect_is(rawData, "tbl")
})
test_that(
"Default data processing steps run until visualisation", {
metaData <- collectMetaData(databaseConnection)
rawData <- collectRawData(con = databaseConnection, id = 1)
plotData <- rawData %>%
imputeMissingIf(input) %>%
addLipidProperties() %>%
standardizeWithinTechnicalReplicatesIf(input) %>%
filterRawDataFor(input) %>%
standardizeWithin(input) %>%
createPlotData(input)
meanPlotData <- summarisePlotData(plotData, input)
plt <- createMainPlot(plotData = plotData,
meanPlotData = meanPlotData,
pairwiseComparisons = NULL,
input = input)
expect_is(plt, "ggplot")
}
)
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