data("convertMsp2Spectra", package = "MetCirc")
spl <- convertMsp2Spectra(msp2spectra)
simMat <- Spectra::compareSpectra(spl, FUN = ndotproduct, m = 0.5, n = 2)
rownames(simMat) <- colnames(simMat) <- spl$name
## START unit test compareSpectra
test_that("compareSpectra", {
expect_equal(sum(simMat), 38.22854, tolerance = 1e-06)
expect_equal(simMat["Isoquercitrin M-H ", "Rutin M-H "], 0.9887026,
tolerance = 1e-06)
})
## END unit test compareSpectra
## START unit test neutralloss
nl <- neutralloss(
matrix(c(unlist(spl[1]$mz), unlist(spl[1]$intensity)), ncol = 2),
matrix(c(unlist(spl[1]$mz), unlist(spl[1]$intensity)), ncol = 2))
test_that("neutralloss", {
expect_equal(nl, 1, tolerance = 1e-6)
simMat_nl <- Spectra::compareSpectra(spl, FUN = neutralloss, m = 0.5, n = 2)
rownames(simMat_nl) <- colnames(simMat_nl) <- spl$name
expect_equal(sum(simMat_nl), 25.9532, tolerance = 1e-04)
expect_equal(simMat_nl["Isoquercitrin M-H ", "Rutin M-H "], 0.182,
tolerance = 1e-03)
})
## END unit test neutralloss
## START unit test orderSimilarityMatrix
simMat_o_mz <- orderSimilarityMatrix(simMat, sps = spl, type = "mz", group = FALSE)
simMat_o_rt <- orderSimilarityMatrix(simMat, sps = spl, type = "retentionTime",
group = FALSE)
simMat_o_cl <- orderSimilarityMatrix(simMat, sps = spl, type = "clustering",
group = FALSE)
## create a matrix with groups
simMat_gr <- simMat
rownames(simMat_gr) <- colnames(simMat_gr) <- paste("A", rownames(simMat),
sep = "_")
test_that("orderSimilarityMatrix", {
expect_error(orderSimilarityMatrix(simMat, sps = spl, type = "foo"),
"'arg' should be one of ")
expect_error(orderSimilarityMatrix(simMat, sps = spl, type = "mz", group = "a"),
"group has to be TRUE or FALSE")
expect_error(orderSimilarityMatrix(type = "mz"),
"is missing, with no default")
expect_error(orderSimilarityMatrix(type = "retentionTime"),
"is missing, with no default")
expect_error(orderSimilarityMatrix(type = "clustering"),
"is missing, with no default")
expect_equal(colnames(simMat_o_mz), spl$name[order(spl$precursorMz)])
expect_equal(rownames(simMat_o_mz), spl$name[order(spl$precursorMz)])
expect_equal(colnames(simMat_o_mz), rownames(simMat_o_mz))
expect_equal(dim(simMat), dim(simMat_o_mz))
expect_true(is.matrix(simMat_o_mz))
expect_true(is.numeric(simMat_o_mz))
expect_equal(colnames(simMat_o_rt), spl$name[order(spl$rtime)])
expect_equal(rownames(simMat_o_rt), spl$name[order(spl$rtime)])
expect_equal(colnames(simMat_o_rt), rownames(simMat_o_rt))
expect_equal(dim(simMat), dim(simMat_o_rt))
expect_true(is.matrix(simMat_o_rt))
expect_true(is.numeric(simMat_o_rt))
expect_equal(colnames(simMat_o_cl), rownames(simMat_o_cl))
expect_equal(dim(simMat), dim(simMat_o_cl))
expect_true(is.matrix(simMat_o_cl))
expect_true(is.numeric(simMat_o_cl))
expect_true(is.matrix(
orderSimilarityMatrix(simMat_gr, sps = spl, type = "mz", group = TRUE)))
expect_true(is.numeric(
orderSimilarityMatrix(simMat_gr, sps = spl, type = "mz", group = TRUE)))
expect_equal(rownames(orderSimilarityMatrix(simMat_gr, sps = spl,
type = "mz", group = TRUE)),
c("A_Chrysin M-H ", "A_Apigenin M-H ", "A_Baicalein M-H ",
"A_Galangin M-H ", "A_Pinostrobin M-H ",
"A_Naringenin M-H ", "A_Acacetin M-H ",
"A_Kaempferol M-H ", "A_Luteolin M-H ",
"A_Quercetin M-H ", "A_Homoeriodictyol M-H ",
"A_Hesperetin M-H ", "A_3-O-methylquercetin M-H ",
"A_Apigetrin M-H ", "A_Avicularin M-H ",
"A_Swertisin M-H ", "A_Isoquercitrin M-H ",
"A_2O-rhamnosyl-swertisin M-H ", "A_Tiliroside M-H ",
"A_Vicenin-2 M-H ", "A_Rutin M-H ", "A_Hesperedin M-H "))
expect_equal(colnames(orderSimilarityMatrix(simMat_gr, sps = spl,
type = "mz", group = TRUE)),
c("A_Chrysin M-H ", "A_Apigenin M-H ", "A_Baicalein M-H ",
"A_Galangin M-H ", "A_Pinostrobin M-H ",
"A_Naringenin M-H ", "A_Acacetin M-H ",
"A_Kaempferol M-H ", "A_Luteolin M-H ",
"A_Quercetin M-H ", "A_Homoeriodictyol M-H ",
"A_Hesperetin M-H ", "A_3-O-methylquercetin M-H ",
"A_Apigetrin M-H ", "A_Avicularin M-H ",
"A_Swertisin M-H ", "A_Isoquercitrin M-H ",
"A_2O-rhamnosyl-swertisin M-H ", "A_Tiliroside M-H ",
"A_Vicenin-2 M-H ", "A_Rutin M-H ", "A_Hesperedin M-H "))
})
## END unit test orderSimilarityMatrix
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