tests/testthat/test-SplatParams.R

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

context("SplatParams")

params <- newSplatParams()

test_that("printing works", {
    expect_output(show(params), "SplatParams")
})

test_that("nBatches checks work", {
    expect_error(
        setParam(params, "nCells", 1),
        "nCells cannot be set directly, set batchCells instead"
    )
    expect_error(
        setParam(params, "nBatches", 1),
        "nBatches cannot be set directly, set batchCells instead"
    )
})

test_that("nGroups checks work", {
    expect_error(
        setParam(params, "nGroups", 1),
        "nGroups cannot be set directly, set group.prob instead"
    )
})

### These tests are also run in test-SplatPopParams.R, please update both
test_that("path.from checks work", {
    pp <- setParams(params, group.prob = c(0.5, 0.5))
    pp <- setParamUnchecked(pp, "path.from", c(0, 1))
    expect_silent(validObject(pp))
    pp <- setParamUnchecked(pp, "path.from", c(0, 3))
    expect_error(validObject(pp), "invalid class")
    pp <- setParamUnchecked(pp, "path.from", c(1, 0))
    expect_error(validObject(pp), "path cannot begin at itself")
    pp <- newSplatParams()
    pp <- setParams(pp, group.prob = c(0.3, 0.3, 0.4))
    pp <- setParamUnchecked(pp, "path.from", c(2, 1, 1))
    expect_error(validObject(pp), "origin must be specified in path.from")
    pp <- setParams(params, group.prob = c(0.5, 0.5), path.from = c(0, 1))
    expect_warning(
        setParam(pp, "group.prob", 1),
        "nGroups has changed, resetting path.from"
    )
    pp <- newSplatParams()
    pp <- setParams(pp, group.prob = c(0.25, 0.25, 0.25, 0.25))
    pp <- setParamUnchecked(pp, "path.from", c(0, 4, 2, 3))
    expect_error(validObject(pp), "path.from cannot contain cycles")
})

### These tests are also run in test-SplatPopParams.R, please update both
test_that("dropout.type checks work", {
    expect_error(
        setParam(params, "dropout.type", "cell"),
        "dropout.type cannot be set to 'cell'"
    )
    pp <- setParams(params,
        dropout.mid = rep(1, 100),
        dropout.shape = rep(1, 100)
    )
    expect_silent(setParam(pp, "dropout.type", "cell"))
    expect_error(
        setParam(params, "dropout.type", "a"),
        "dropout.type must be one of: "
    )
})

test_that("setParams order doesn't matter", {
    expect_silent(setParams(params,
        group.prob = c(0.5, 0.5),
        de.facLoc = c(0.1, 5)
    ))
    expect_silent(setParams(params,
        de.facLoc = c(0.1, 5),
        group.prob = c(0.5, 0.5)
    ))
})

test_that("group.prob gets rescaled", {
    expect_warning(
        setParams(params, group.prob = 1:3),
        "group.prob does not sum to 1 and will be rescaled"
    )
})

test_that("group.prob sum check works", {
    probs <- runif(10)
    probs <- probs / sum(probs)
    expect_silent(setParams(params, group.prob = probs))
    pp <- setParamUnchecked(params, "group.prob", 1:3)
    expect_error(validObject(pp), "group.probs must sum to 1")
})