Nothing
context("determineWarpingFunctions")
r <- createMassPeaks(mass=1:10, intensity=1:10)
p <- createMassPeaks(mass=(1:10)+0.01, intensity=1:10)
test_that("determineWarpingFunctions throws errors", {
expect_error(determineWarpingFunctions(1:10),
"no list of MALDIquant::MassPeaks objects")
expect_error(determineWarpingFunctions(p, reference=createMassPeaks(double(),
double())),
"Reference MassPeaks object contains no peaks")
expect_error(determineWarpingFunctions(createMassPeaks(mass=20, intensity=20),
reference=r),
"Could not match any peak in spectrum 1 to a reference peak")
})
test_that("determineWarpingFunctions throws warnings", {
expect_warning(determineWarpingFunctions(p, reference=r[6:10]),
"Reference MassPeaks object contains very few peaks")
expect_error(tryCatch(determineWarpingFunctions(list(p, p), plot=TRUE),
warning=function(w)stop(conditionMessage(w))),
paste0(".*plot.* is .*TRUE.* but no non-interactive device ",
"is available. Using pdf.* to create a default one."))
expect_error(tryCatch(determineWarpingFunctions(list(p, p), plot=TRUE,
plotInteractive=TRUE),
warning=function(w)stop(conditionMessage(w))),
paste0(".*plot.* is .*TRUE.* but no interactive device is ",
"available. Using dev.new.* to create a default one."))
expect_warning(determineWarpingFunctions(list(p, createMassPeaks(11, 11)),
reference=r, allowNoMatches=TRUE),
"Could not match any peak in spectrum 2 to a reference peak")
})
test_that("determineWarpingFunctions works with single MassPeaks object", {
w <- determineWarpingFunctions(p, reference=r, method="linear")
expect_equal(attr(w, "nmatch"), 6)
wp <- warpMassPeaks(list(p), w)[[1]]
expect_equal(r, wp)
})
test_that("determineWarpingFunctions works with list of MassPeaks objects", {
w <- determineWarpingFunctions(list(a=p, b=p), reference=r, method="linear")
expect_equal(attr(w, "nmatch"), c(a=6, b=6))
wp <- warpMassPeaks(list(p, p), w)
expect_equal(list(r, r), wp)
})
test_that("determineWarpingFunctions supports allowNoMatches argument", {
suppressWarnings(
w <- determineWarpingFunctions(
list(p, createMassPeaks(11, 11), p), reference=r, allowNoMatches=TRUE)
)
expect_equal(sapply(w, is.function), c(TRUE, FALSE, TRUE))
expect_equal(is.na(w), c(FALSE, TRUE, FALSE))
expect_equal(attr(w, "nmatch"), c(6, 0, 6))
wp <- warpMassPeaks(list(p, createMassPeaks(11, 11), p), w, emptyNoMatches=TRUE)
expect_equal(list(r, createMassPeaks(11, 0), r), wp)
})
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