tests/testthat/test_structural.R
In tnaake/MetNet: Inferring metabolic networks from untargeted high-resolution mass spectrometry data
## create toy example data set
data("mat_test", package = "MetNet")
colnames(mat_test) <- paste0("intensity_", 1:20)
mz <- c(100, 150, 262.0528, 262.0528, 262.0528, 348.0532, 448.0532)
rt <- c(100, 100, 50, 150, 150, 150, 150)
mat_test <- cbind(mz = mz, rt = rt, mat_test)
rownames(mat_test) <- paste(mz, rt, sep = "_")
mat_test_old <- mat_test
# test the case when the transformation list is a tibble object
## transformations object for structural calculation
transformations <-
rbind(c("Malonyl group (-H2O)", "C3H2O3", 86.0003939305, "+"),
c("Monosaccharide (-H2O)", "C6H10O5", 162.0528234315, "-"))
transformations_neg <- transformations <-
tibble::as_tibble(data.frame(
group = transformations[, 1],
formula = transformations[, 2],
mass = as.numeric(transformations[, 3]),
rt = transformations[, 4]))
transformations_neg[, 3] <- -1 * transformations_neg[, 3]
## START unit test structural ##
struct_adj_old <- struct_adj <-
structural(
mat_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE
)
struct_adj_neg <-
structural(
mat_test, transformation = transformations_neg,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE
)
struct_adj_dir_old <- struct_adj_dir <-
structural(
mat_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE
)
struct_adj_dir_neg <-
structural(
mat_test, transformation = transformations_neg,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE
)
g_undir <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj, "binary", mode = "directed", weighted = NULL)
)
g_undir_neg <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_neg, "binary", mode = "directed", weighted = NULL)
)
g_dir <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir, "binary"), mode = "directed", weighted = NULL
)
g_dir_neg <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir_neg, "binary"), mode = "directed", weighted = NULL
)
plot(g_undir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_undir_neg, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir_neg, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
test_that("structural", {
expect_error(structural(mat_test[, -1], transformations),
"does not contain the column mz")
expect_error(structural(NULL, transformations),
"'x' has to be a matrix or data.frame")
expect_error(structural(mat_test, transformations[, -3]),
"does not contain the column mass")
expect_error(structural(mat_test, matrix()),
"is not a data.frame")
expect_error(structural(mat_test, transformations, ppm = "a"),
"'ppm' has to be a numeric of length 1")
expect_error(structural(mat_test, transformations, var = c("group", "foo")),
"'transformation' does not contain the column 'foo'")
expect_error(structural(mat_test, transformations, var = "foo"),
"'transformation' does not contain the column 'foo'")
expect_error(structural(mat_test, transformations,
var = c("group", "foo", "foo2")),
"'transformation' does not contain the column 'foo', 'foo2'")
expect_error(structural(mat_test, transformations, var = c("foo", "foo2")),
"'transformation' does not contain the column 'foo', 'foo2'")
expect_error(structural(mat_test, transformations, var = ""),
"'transformation' does not contain the column ''")
expect_error(structural(mat_test, transformations, var = NULL),
"'var' is not a character vector")
expect_error(structural(mat_test, transformations, var = numeric()),
"'var' is not a character vector")
expect_error(structural(mat_test, transformations, var = logical()),
"'var' is not a character vector")
expect_equal(assayNames(structural(mat_test, transformations,
var = character())), "binary")
expect_true(validObject(struct_adj))
expect_equal(assayNames(struct_adj), c("binary", "group", "formula", "mass"))
expect_equal(length(struct_adj), 7)
expect_equal(dim(struct_adj), c(7, 7))
expect_equal(dim(assay(struct_adj, "binary")), c(7, 7))
expect_equal(dim(assay(struct_adj, "group")), c(7, 7))
expect_equal(dim(assay(struct_adj, "formula")), c(7, 7))
expect_equal(dim(assay(struct_adj, "mass")), c(7, 7))
expect_equal(rownames(assay(struct_adj, 1)), colnames(assay(struct_adj, 1)))
expect_equal(rownames(assay(struct_adj, 2)), colnames(assay(struct_adj, 2)))
expect_equal(rownames(assay(struct_adj, 3)), rownames(assay(struct_adj, 3)))
expect_equal(rownames(assay(struct_adj, 4)), rownames(assay(struct_adj, 4)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 2)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 3)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 4)))
expect_equal(rownames(assay(struct_adj, 1)), paste(mz, rt, sep = "_"))
expect_equal(sum(assay(struct_adj, "binary")), 12)
expect_equal(sum(assay(struct_adj_neg, "binary")), 0)
expect_equal(sum(assay(struct_adj_dir, "binary")), 6)
expect_equal(sum(assay(struct_adj_dir_neg, "binary")), 6)
expect_equal(as.vector(assay(struct_adj, "group")[, 1]),
c("", "", "Monosaccharide (-H2O)", "Monosaccharide (-H2O)",
"Monosaccharide (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 3]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 4]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 5]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 6]),
c("", "", "Malonyl group (-H2O)", "Malonyl group (-H2O)",
"Malonyl group (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 1]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 3]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 4]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 5]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 6]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 1]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 3]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 4]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 5]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 6]),
c("", "", "Malonyl group (-H2O)", "Malonyl group (-H2O)",
"Malonyl group (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 1]),
c("", "", "Monosaccharide (-H2O)", "Monosaccharide (-H2O)",
"Monosaccharide (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 3]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 4]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 5]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 6]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(unique(as.vector(assay(struct_adj, "group"))),
c("", "Monosaccharide (-H2O)", "Malonyl group (-H2O)"))
expect_equal(unique(as.vector(assay(struct_adj, "mass"))),
c("", "162.0528234315", "86.0003939305"))
expect_equal(unique(as.vector(assay(struct_adj, "formula"))),
c("", "C6H10O5", "C3H2O3"))
expect_true(is.matrix(assay(struct_adj, "binary")))
expect_true(is.matrix(assay(struct_adj, "group")))
expect_true(is.matrix(assay(struct_adj, "mass")))
expect_true(is.matrix(assay(struct_adj, "formula")))
expect_true(is.numeric(assay(struct_adj, "binary")))
expect_true(is.character(assay(struct_adj, "group")))
expect_true(is.character(assay(struct_adj, "mass")))
expect_true(is.character(assay(struct_adj, "formula")))
expect_equal(struct_adj@directed, FALSE)
expect_equal(struct_adj_neg@directed, FALSE)
expect_equal(struct_adj_dir@directed, TRUE)
expect_equal(struct_adj_dir_neg@directed, TRUE)
expect_equal(struct_adj@type, "structural")
expect_equal(struct_adj_neg@type, "structural")
expect_equal(struct_adj_dir@type, "structural")
expect_equal(struct_adj_dir_neg@type, "structural")
expect_equal(struct_adj@thresholded, FALSE)
expect_equal(struct_adj_neg@thresholded, FALSE)
expect_equal(struct_adj_dir@thresholded, FALSE)
expect_equal(struct_adj_dir_neg@thresholded, FALSE)
## test for mass difference value of 0
mat_test <- mat_test_old
mat_test[,"mz"] <-
c(100, 150, 262.0528, 262.0528, 262.0528, 348.0532, 448.0532)
mat_test[, "rt"] <- c(100, 100, 50, 150, 151, 150, 150)
rownames(mat_test) <- paste(mat_test[, "mz"], mat_test[, "rt"], sep = "_")
transformations_0 <- data.frame(
group = "no transformation", formula = "", mass = 0, rt = "?")
struct_adj_dir <- structural(mat_test, transformation = transformations_0,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE)
struct_adj_undir <- structural(mat_test, transformation = transformations_0,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE)
a_dir <- assay(struct_adj_dir, "binary")
a_undir <- assay(struct_adj_undir, "binary")
expect_equal(sum(a_dir), 13)
expect_equal(as.vector(a_dir["100_100", ]), c(1, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["150_100", ]), c(0, 1, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["262.0528_50", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["262.0528_150", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["262.0528_151", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["348.0532_150", ]), c(0, 0, 0, 0, 0, 1, 0))
expect_equal(as.vector(a_dir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(sum(a_undir), 13)
expect_equal(as.vector(a_undir["100_100", ]), c(1, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["150_100", ]), c(0, 1, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["262.0528_50", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["262.0528_150", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["262.0528_151", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["348.0532_150", ]), c(0, 0, 0, 0, 0, 1, 0))
expect_equal(as.vector(a_undir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
## another test with transformation slighty > 0 and very small ppm
mat_test <- mat_test_old
mat_test[, "mz"] <- c(100, 150, 262.0528, 263.0528, 263.0538, 448.0532, 448.0542)
mat_test[, "rt"] <- c(100, 100, 50, 150, 151, 150, 150)
rownames(mat_test) <- paste(mat_test[, "mz"], mat_test[, "rt"], sep = "_")
transformations_1 <- data.frame(
group = "no transformation", formula = "", mass = 0.001,
rt = "?")
struct_adj_dir <- structural(mat_test, transformation = transformations_1,
var = c("group", "formula", "mass"), ppm = 1, directed = TRUE)
struct_adj_undir <- structural(mat_test, transformation = transformations_1,
var = c("group", "formula", "mass"), ppm = 1, directed = FALSE)
a_dir <- assay(struct_adj_dir, "binary")
a_undir <- assay(struct_adj_undir, "binary")
expect_equal(sum(a_dir), 2)
expect_equal(as.vector(a_dir["100_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["150_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["262.0528_50", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["263.0528_150", ]), c(0, 0, 0, 0, 1, 0, 0))
expect_equal(as.vector(a_dir["263.0538_151", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(as.vector(a_dir["448.0542_150", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(sum(a_undir), 4)
expect_equal(as.vector(a_undir["100_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["150_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["262.0528_50", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["263.0528_150", ]), c(0, 0, 0, 0, 1, 0, 0))
expect_equal(as.vector(a_undir["263.0538_151", ]), c(0, 0, 0, 1, 0, 0, 0))
expect_equal(as.vector(a_undir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(as.vector(a_undir["448.0542_150", ]), c(0, 0, 0, 0, 0, 1, 0))
})
## transformations object for structural calculation
transformations <- rbind(
c("Malonyl group (-H2O)", "C3H2O3", 86.0003939305, "+"),
c("Monosaccharide (-H2O)", "C6H10O5", 162.0528234315, "-"))
transformations_neg <- transformations_old <- transformations <- data.frame(
group = transformations[, 1],
formula = transformations[, 2],
mass = as.numeric(transformations[, 3]),
rt = transformations[, 4])
transformations_neg[, 3] <- -1 * transformations_neg[, 3]
## START unit test structural ##
struct_adj_old <- struct_adj <- structural(mat_test,
transformation = transformations, var = c("group", "formula", "mass"),
ppm = 5, directed = FALSE)
struct_adj_neg <- structural(mat_test, transformation = transformations_neg,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE)
struct_adj_dir_old <- struct_adj_dir <- structural(mat_test,
transformation = transformations, var = c("group", "formula", "mass"),
ppm = 5, directed = TRUE)
struct_adj_dir_neg <- structural(mat_test, transformation = transformations_neg,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE)
g_undir <- igraph::graph_from_adjacency_matrix(
assay(struct_adj, "binary", mode = "directed", weighted = NULL))
g_undir_neg <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_neg, "binary", mode = "directed", weighted = NULL))
g_dir <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir, "binary"), mode = "directed", weighted = NULL)
g_dir_neg <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir_neg, "binary"), mode = "directed", weighted = NULL)
plot(g_undir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_undir_neg, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir_neg, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
test_that("structural", {
expect_error(structural(mat_test[, -1], transformations),
"does not contain the column mz")
expect_error(structural(NULL, transformations),
"'x' has to be a matrix or data.frame")
expect_error(structural(mat_test, transformations[, -3]),
"does not contain the column mass")
expect_error(structural(mat_test, matrix()),
"is not a data.frame")
expect_error(structural(mat_test, transformations, ppm = "a"),
"'ppm' has to be a numeric of length 1")
expect_error(structural(mat_test, transformations, var = c("group", "foo")),
"'transformation' does not contain the column 'foo'")
expect_error(structural(mat_test, transformations, var = "foo"),
"'transformation' does not contain the column 'foo'")
expect_error(structural(mat_test, transformations,
var = c("group", "foo", "foo2")),
"'transformation' does not contain the column 'foo', 'foo2'")
expect_error(structural(mat_test, transformations,
var = c("foo", "foo2")),
"'transformation' does not contain the column 'foo', 'foo2'")
expect_error(structural(mat_test, transformations, var = ""),
"'transformation' does not contain the column ''")
expect_error(structural(mat_test, transformations, var = NULL),
"'var' is not a character vector")
expect_error(structural(mat_test, transformations, var = numeric()),
"'var' is not a character vector")
expect_error(structural(mat_test, transformations, var = logical()),
"'var' is not a character vector")
expect_equal(assayNames(structural(mat_test, transformations,
var = character())), "binary")
expect_true(validObject(struct_adj))
expect_equal(assayNames(struct_adj),
c("binary", "group", "formula", "mass"))
expect_equal(length(struct_adj), 7)
expect_equal(dim(struct_adj), c(7, 7))
expect_equal(dim(assay(struct_adj, "binary")), c(7, 7))
expect_equal(dim(assay(struct_adj, "group")), c(7, 7))
expect_equal(dim(assay(struct_adj, "formula")), c(7, 7))
expect_equal(dim(assay(struct_adj, "mass")), c(7, 7))
expect_equal(rownames(assay(struct_adj, 1)), colnames(assay(struct_adj, 1)))
expect_equal(rownames(assay(struct_adj, 2)), colnames(assay(struct_adj, 2)))
expect_equal(rownames(assay(struct_adj, 3)), rownames(assay(struct_adj, 3)))
expect_equal(rownames(assay(struct_adj, 4)), rownames(assay(struct_adj, 4)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 2)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 3)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 4)))
expect_equal(rownames(assay(struct_adj, 1)), paste(mz, rt, sep = "_"))
expect_equal(sum(assay(struct_adj, "binary")), 12)
expect_equal(sum(assay(struct_adj_neg, "binary")), 0)
expect_equal(sum(assay(struct_adj_dir, "binary")), 6)
expect_equal(sum(assay(struct_adj_dir_neg, "binary")), 6)
expect_equal(as.vector(assay(struct_adj, "group")[, 1]),
c("", "", "Monosaccharide (-H2O)", "Monosaccharide (-H2O)",
"Monosaccharide (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 3]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 4]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 5]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 6]),
c("", "", "Malonyl group (-H2O)", "Malonyl group (-H2O)",
"Malonyl group (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 1]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 3]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 4]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 5]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 6]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 1]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 3]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 4]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 5]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 6]),
c("", "", "Malonyl group (-H2O)", "Malonyl group (-H2O)",
"Malonyl group (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 1]),
c("", "", "Monosaccharide (-H2O)", "Monosaccharide (-H2O)",
"Monosaccharide (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 3]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 4]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 5]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 6]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(unique(as.vector(assay(struct_adj, "group"))),
c("", "Monosaccharide (-H2O)", "Malonyl group (-H2O)"))
expect_equal(unique(as.vector(assay(struct_adj, "mass"))),
c("", "162.0528234315", "86.0003939305"))
expect_equal(unique(as.vector(assay(struct_adj, "formula"))),
c("", "C6H10O5", "C3H2O3"))
expect_true(is.matrix(assay(struct_adj, "binary")))
expect_true(is.matrix(assay(struct_adj, "group")))
expect_true(is.matrix(assay(struct_adj, "mass")))
expect_true(is.matrix(assay(struct_adj, "formula")))
expect_true(is.numeric(assay(struct_adj, "binary")))
expect_true(is.character(assay(struct_adj, "group")))
expect_true(is.character(assay(struct_adj, "mass")))
expect_true(is.character(assay(struct_adj, "formula")))
expect_equal(struct_adj@directed, FALSE)
expect_equal(struct_adj_neg@directed, FALSE)
expect_equal(struct_adj_dir@directed, TRUE)
expect_equal(struct_adj_dir_neg@directed, TRUE)
expect_equal(struct_adj@type, "structural")
expect_equal(struct_adj_neg@type, "structural")
expect_equal(struct_adj_dir@type, "structural")
expect_equal(struct_adj_dir_neg@type, "structural")
expect_equal(struct_adj@thresholded, FALSE)
expect_equal(struct_adj_neg@thresholded, FALSE)
expect_equal(struct_adj_dir@thresholded, FALSE)
expect_equal(struct_adj_dir_neg@thresholded, FALSE)
## test for mass difference value of 0
mat_test <- mat_test_old
mat_test[,"mz"] <- c(100, 150, 262.0528, 262.0528, 262.0528, 348.0532, 448.0532)
mat_test[, "rt"] <- c(100, 100, 50, 150, 151, 150, 150)
rownames(mat_test) <- paste(mat_test[, "mz"], mat_test[, "rt"], sep = "_")
transformations_0 <- data.frame(
group = "no transformation", formula = "", mass = 0, rt = "?")
struct_adj_dir <- structural(mat_test, transformation = transformations_0,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE)
struct_adj_undir <- structural(mat_test, transformation = transformations_0,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE)
a_dir <- assay(struct_adj_dir, "binary")
a_undir <- assay(struct_adj_undir, "binary")
expect_equal(sum(a_dir), 13)
expect_equal(as.vector(a_dir["100_100", ]), c(1, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["150_100", ]), c(0, 1, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["262.0528_50", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["262.0528_150", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["262.0528_151", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["348.0532_150", ]), c(0, 0, 0, 0, 0, 1, 0))
expect_equal(as.vector(a_dir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(sum(a_undir), 13)
expect_equal(as.vector(a_undir["100_100", ]), c(1, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["150_100", ]), c(0, 1, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["262.0528_50", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["262.0528_150", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["262.0528_151", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["348.0532_150", ]), c(0, 0, 0, 0, 0, 1, 0))
expect_equal(as.vector(a_undir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
## another test with transformation slighty > 0 and very small ppm
mat_test <- mat_test_old
mat_test[, "mz"] <- c(100, 150, 262.0528, 263.0528, 263.0538, 448.0532, 448.0542)
mat_test[, "rt"] <- c(100, 100, 50, 150, 151, 150, 150)
rownames(mat_test) <- paste(mat_test[, "mz"], mat_test[, "rt"], sep = "_")
transformations_1 <- data.frame(
group = "no transformation", formula = "", mass = 0.001,
rt = "?")
struct_adj_dir <- structural(mat_test, transformation = transformations_1,
var = c("group", "formula", "mass"), ppm = 1, directed = TRUE)
struct_adj_undir <- structural(mat_test, transformation = transformations_1,
var = c("group", "formula", "mass"), ppm = 1, directed = FALSE)
a_dir <- assay(struct_adj_dir, "binary")
a_undir <- assay(struct_adj_undir, "binary")
expect_equal(sum(a_dir), 2)
expect_equal(as.vector(a_dir["100_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["150_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["262.0528_50", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["263.0528_150", ]), c(0, 0, 0, 0, 1, 0, 0))
expect_equal(as.vector(a_dir["263.0538_151", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(as.vector(a_dir["448.0542_150", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(sum(a_undir), 4)
expect_equal(as.vector(a_undir["100_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["150_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["262.0528_50", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["263.0528_150", ]), c(0, 0, 0, 0, 1, 0, 0))
expect_equal(as.vector(a_undir["263.0538_151", ]), c(0, 0, 0, 1, 0, 0, 0))
expect_equal(as.vector(a_undir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(as.vector(a_undir["448.0542_150", ]), c(0, 0, 0, 0, 0, 1, 0))
})
## END unit test structural ##
## START unit test rtCorrection ##
struct_adj <- struct_adj_old
struct_adj_dir <- struct_adj_dir_old
mat_test <- mat_test_old
transformations <- transformations_old
struct_adj_rt <- rtCorrection(struct_adj, mat_test, transformations,
var = "group")
struct_adj_rt_dir <- rtCorrection(struct_adj_dir, mat_test, transformations,
var = "group")
g_undir <- igraph::graph_from_adjacency_matrix(
assay(struct_adj, "binary", mode = "directed", weighted = NULL))
g_undir_rt <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_rt, "binary", mode = "directed", weighted = NULL))
g_dir <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir, "binary"), mode = "directed", weighted = NULL)
g_dir_rt <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_rt_dir, "binary"), mode = "directed", weighted = NULL)
plot(g_undir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_undir_rt, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir_rt, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
test_that("rtCorrection", {
expect_error(rtCorrection(struct_adj[[1]], mat_test, transformations),
"is not an 'AdjacencyMatrix'")
tmp <- struct_adj
assay(tmp, "transformation") <- assay(tmp, "binary")
expect_error(rtCorrection(tmp, mat_test, transformations),
"must be character")
tmp <- struct_adj
assay(tmp, "mass") <- assay(tmp, "binary")
expect_error(rtCorrection(tmp, mat_test, transformations),
"must be character")
expect_error(rtCorrection(struct_adj, NULL, transformations),
"'x' does not contain the column 'rt'")
expect_error(rtCorrection(struct_adj, mat_test[, -1], transformations),
"'x' does not contain the column 'mz'")
expect_error(rtCorrection(struct_adj, mat_test[, -2], transformations),
"'x' does not contain the column 'rt'")
expect_error(rtCorrection(struct_adj, mat_test, NULL),
"'transformation' does not contain the column 'group'")
expect_error(rtCorrection(struct_adj, mat_test, transformations[, -1]),
"'transformation' does not contain the column 'group'")
expect_error(rtCorrection(struct_adj, mat_test, transformations[, -4]),
"'transformation' does not contain the column 'rt'")
expect_error(rtCorrection(struct_adj, mat_test,
transformation = cbind(transformations[, -4], rt = rep("a", 2))),
"does contain other")
expect_true(is.matrix(assay(struct_adj_rt, "binary")))
expect_true(is.numeric(assay(struct_adj_rt, "binary")))
expect_true(is.matrix(assay(struct_adj_rt, "group")))
expect_true(is.character(assay(struct_adj_rt, "group")))
expect_true(is.matrix(assay(struct_adj_rt, "mass")))
expect_true(is.character(assay(struct_adj_rt, "mass")))
expect_true(is.matrix(assay(struct_adj_rt, "formula")))
expect_true(is.character(assay(struct_adj_rt, "formula")))
expect_equal(colnames(assay(struct_adj_rt, "binary")),
paste(mz, rt, sep = "_"))
expect_equal(colnames(assay(struct_adj_rt, 1)),
rownames(assay(struct_adj_rt, 1)))
expect_equal(colnames(assay(struct_adj_rt, 2)),
rownames(assay(struct_adj_rt, 2)))
expect_equal(colnames(assay(struct_adj_rt, 3)),
rownames(assay(struct_adj_rt, 3)))
expect_equal(colnames(assay(struct_adj_rt, 1)),
colnames(assay(struct_adj_rt, 2)))
expect_equal(colnames(assay(struct_adj_rt, 1)),
colnames(assay(struct_adj_rt, 3)))
expect_true(table(assay(struct_adj_rt, "binary"))[1] == 41)
expect_true(table(assay(struct_adj_rt_dir, "binary"))[1] == 45)
expect_equal(sum(assay(struct_adj_rt, "binary")), 8)
expect_equal(sum(assay(struct_adj_rt_dir, "binary")), 4)
expect_true(all(
table(assay(struct_adj_rt, "group")) == c(41, 6, 2)))
expect_true(all(
table(assay(struct_adj_rt, "mass")) == c(41, 2, 6)))
expect_true(all(
table(assay(struct_adj_rt, "formula")) == c(41, 6, 2)))
expect_true(all(
table(assay(struct_adj_rt_dir, "group")) == c(45, 3, 1)))
expect_true(all(
table(assay(struct_adj_rt_dir, "mass")) == c(45, 1, 3)))
expect_true(all(
table(assay(struct_adj_rt_dir, "formula")) == c(45, 3, 1)))
expect_equal(directed(struct_adj_rt), FALSE)
expect_equal(directed(struct_adj_rt_dir), TRUE)
expect_equal(type(struct_adj_rt), "structural")
expect_equal(type(struct_adj_rt_dir), "structural")
expect_equal(thresholded(struct_adj_rt), TRUE)
expect_equal(thresholded(struct_adj_rt_dir), TRUE)
## create a double assignment to certain cells
transformations <- rbind(transformations,
data.frame(group = "pseudo Monosaccharide",
formula = "C6H10O5", mass = 162.05282, rt = "?"))
struct_adj_pseudo <- structural(mat_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE)
expect_equal(assay(struct_adj_pseudo, "group")[3, 1],
"Monosaccharide (-H2O)/pseudo Monosaccharide")
expect_equal(assay(struct_adj_pseudo, "mass")[3, 1],
"162.0528234315/162.05282")
expect_equal(assay(struct_adj_pseudo, "formula")[3, 1],
"C6H10O5/C6H10O5")
struct_adj_pseudo_rt <- rtCorrection(struct_adj_pseudo, x = mat_test,
transformation = transformations, var = "group")
})
## test rtCorrection with the transformation table as tibble
struct_adj <- struct_adj_old
struct_adj_dir <- struct_adj_dir_old
mat_test <- mat_test_old
transformations <- tibble::as_tibble(transformations_old)
struct_adj_rt <-
rtCorrection(struct_adj, mat_test, transformations, var = "group")
struct_adj_rt_dir <-
rtCorrection(struct_adj_dir, mat_test, transformations, var = "group")
g_undir <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj, "binary", mode = "directed", weighted = NULL)
)
g_undir_rt <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_rt, "binary", mode = "directed", weighted = NULL)
)
g_dir <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir, "binary"), mode = "directed", weighted = NULL
)
g_dir_rt <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_rt_dir, "binary"), mode = "directed", weighted = NULL
)
plot(
g_undir, edge.width = 1, edge.arrow.size = 0.5, vertex.label.cex = 0.8,
edge.color = "grey"
)
plot(
g_undir_rt, edge.width = 1, edge.arrow.size = 0.5, vertex.label.cex = 0.8,
edge.color = "grey"
)
plot(
g_dir, edge.width = 1, edge.arrow.size = 0.5, vertex.label.cex = 0.8,
edge.color = "grey"
)
plot(
g_dir_rt, edge.width = 1, edge.arrow.size = 0.5, vertex.label.cex = 0.8,
edge.color = "grey"
)
test_that("rtCorrection", {
expect_error(
rtCorrection(struct_adj[[1]], mat_test, transformations),
"is not an 'AdjacencyMatrix'"
)
tmp <- struct_adj
assay(tmp, "transformation") <- assay(tmp, "binary")
expect_error(
rtCorrection(tmp, mat_test, transformations), "must be character"
)
tmp <- struct_adj
assay(tmp, "mass") <- assay(tmp, "binary")
expect_error(
rtCorrection(tmp, mat_test, transformations), "must be character"
)
expect_error(
rtCorrection(struct_adj, NULL, transformations),
"'x' does not contain the column 'rt'"
)
expect_error(
rtCorrection(struct_adj, mat_test[, -1], transformations),
"'x' does not contain the column 'mz'"
)
expect_error(
rtCorrection(struct_adj, mat_test[, -2], transformations),
"'x' does not contain the column 'rt'"
)
expect_error(
rtCorrection(struct_adj, mat_test, NULL),
"'transformation' does not contain the column 'group'"
)
expect_error(
rtCorrection(struct_adj, mat_test, transformations[, -1]),
"'transformation' does not contain the column 'group'"
)
expect_error(
rtCorrection(struct_adj, mat_test, transformations[, -4]),
"'transformation' does not contain the column 'rt'"
)
expect_error(
rtCorrection(
struct_adj, mat_test,
transformation = cbind(transformations[, -4], rt = rep("a", 2))
), "does contain other"
)
expect_true(is.matrix(assay(struct_adj_rt, "binary")))
expect_true(is.numeric(assay(struct_adj_rt, "binary")))
expect_true(is.matrix(assay(struct_adj_rt, "group")))
expect_true(is.character(assay(struct_adj_rt, "group")))
expect_true(is.matrix(assay(struct_adj_rt, "mass")))
expect_true(is.character(assay(struct_adj_rt, "mass")))
expect_true(is.matrix(assay(struct_adj_rt, "formula")))
expect_true(is.character(assay(struct_adj_rt, "formula")))
expect_equal(
colnames(assay(struct_adj_rt, "binary")), paste(mz, rt, sep = "_")
)
expect_equal(
colnames(assay(struct_adj_rt, 1)), rownames(assay(struct_adj_rt, 1))
)
expect_equal(
colnames(assay(struct_adj_rt, 2)), rownames(assay(struct_adj_rt, 2))
)
expect_equal(
colnames(assay(struct_adj_rt, 3)), rownames(assay(struct_adj_rt, 3))
)
expect_equal(
colnames(assay(struct_adj_rt, 1)), colnames(assay(struct_adj_rt, 2))
)
expect_equal(
colnames(assay(struct_adj_rt, 1)), colnames(assay(struct_adj_rt, 3))
)
expect_true(table(assay(struct_adj_rt, "binary"))[1] == 41)
expect_true(table(assay(struct_adj_rt_dir, "binary"))[1] == 45)
expect_equal(sum(assay(struct_adj_rt, "binary")), 8)
expect_equal(sum(assay(struct_adj_rt_dir, "binary")), 4)
expect_true(all(table(assay(struct_adj_rt, "group")) == c(41, 6, 2)))
expect_true(all(table(assay(struct_adj_rt, "mass")) == c(41, 2, 6)))
expect_true(all(table(assay(struct_adj_rt, "formula")) == c(41, 6, 2)))
expect_true(all(table(assay(struct_adj_rt_dir, "group")) == c(45, 3, 1)))
expect_true(all(table(assay(struct_adj_rt_dir, "mass")) == c(45, 1, 3)))
expect_true(all(table(assay(struct_adj_rt_dir, "formula")) == c(45, 3, 1)))
expect_equal(directed(struct_adj_rt), FALSE)
expect_equal(directed(struct_adj_rt_dir), TRUE)
expect_equal(type(struct_adj_rt), "structural")
expect_equal(type(struct_adj_rt_dir), "structural")
expect_equal(thresholded(struct_adj_rt), TRUE)
expect_equal(thresholded(struct_adj_rt_dir), TRUE)
## create a double assignment to certain cells
transformations <-
rbind(
transformations,
data.frame(
group = "pseudo Monosaccharide", formula = "C6H10O5", mass = 162.05282,
rt = "?"
)
)
struct_adj_pseudo <-
structural(
mat_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE
)
expect_equal(
assay(struct_adj_pseudo, "group")[3, 1],
"Monosaccharide (-H2O)/pseudo Monosaccharide"
)
expect_equal(
assay(struct_adj_pseudo, "mass")[3, 1], "162.0528234315/162.05282"
)
expect_equal(assay(struct_adj_pseudo, "formula")[3, 1], "C6H10O5/C6H10O5")
struct_adj_pseudo_rt <-
rtCorrection(
struct_adj_pseudo, x = mat_test, transformation = transformations,
var = "group"
)
})
## END unit test rtCorrection ##
## create toy example data set
data("x_test", package = "MetNet")
x_test <- as.matrix(x_test)
## transformations object for structural calculation
transformations <- rbind(
c("Malonyl group (-H2O)", "C3H2O3", "86.0003939305"),
c("Monosaccharide (-H2O)", "C6H10O5", "162.0528234315"))
transformations <- data.frame(group = as.character(transformations[, 1]),
formula = as.character(transformations[, 2]),
mass = as.numeric(transformations[, 3]))
## create structural network
struct_adj <- structural(x_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5)
## create statistical network
stat_adj <- statistical(x_test[, -c(1:2)],
model = c("clr", "aracne", "pearson", "spearman", "ggm"))
stat_adj_thr <- threshold(stat_adj, type = "top2", args = list(n = 10))
## load MS2
f <- system.file("spectra_matrix/spectra_matrix.RDS", package = "MetNet")
adj_spec <- readRDS(f)
## START unit test spectral similarity ##
spect_adj <- addSpectralSimilarity(am_structural = struct_adj,
ms2_similarity = list("ndotproduct" = adj_spec))
test_that("addSpectralSimilarity", {
expect_error(addSpectralSimilarity(adj_spec, NULL),
"'am_structural' is not an 'AdjacencyMatrix' object")
expect_true(validObject(spect_adj))
expect_equal(assayNames(spect_adj),
c("binary", "group", "formula", "mass", "ndotproduct"))
expect_equal(sum(assay(spect_adj, "ndotproduct"), na.rm = TRUE),
45.16721, tolerance = 5e-01)
expect_equal(as.vector(assay(spect_adj, "ndotproduct")[7, 1:10]),
c(0, 0, 0, 0.989282368, 0, 0, 1, 0.003863543, 0, 0))
expect_equal(rownames(assay(spect_adj, "ndotproduct")),
colnames(assay(spect_adj, "ndotproduct")))
expect_equal(rownames(assay(spect_adj, "ndotproduct")),
colnames(assay(struct_adj, "binary")))
expect_true(is.numeric(assay(spect_adj, "ndotproduct")))
})
## test threshold() and combine()
args_thr <- list(filter = "ndotproduct > 0.1 |
binary == 1 & is.na(ndotproduct)")
thr_thr <- threshold(spect_adj, type = "threshold", args = args_thr)
cons_adj <- combine(thr_thr, stat_adj_thr)
test_that("threshold and combine similarity", {
expect_error(threshold(spect_adj, type = "top1", args = list(n = 2)),
"'am' 'structural' can only be thresholded by 'type = threshold'")
expect_true(is(thr_thr, "AdjacencyMatrix"))
expect_equal(assayNames(thr_thr),
c("binary", "group", "formula", "mass", "ndotproduct"))
expect_true(is.numeric(assay(thr_thr, "binary")))
expect_equal(rownames(assay(thr_thr, "binary")),
rownames(assay(spect_adj, "binary")))
expect_equal(colnames(assay(thr_thr, "binary")),
colnames(assay(spect_adj, "binary")))
expect_equal(sum(assay(thr_thr, "binary"), na.rm = TRUE), 60)
expect_true(all(assay(thr_thr, "binary") %in% c(0, 1, NaN)))
## test combine
expect_true(validObject(cons_adj))
expect_equal(assayNames(cons_adj),
c("binary", "group", "formula", "mass", "ndotproduct",
"clr_coef", "aracne_coef", "pearson_coef", "pearson_pvalue",
"spearman_coef", "spearman_pvalue", "ggm_coef", "ggm_pvalue",
"consensus", "combine_binary", "combine_group",
"combine_formula", "combine_mass", "combine_ndotproduct"))
expect_equal(sum(assay(cons_adj, "combine_binary"), na.rm = TRUE), 4)
expect_equal(as.vector(assay(cons_adj, "combine_binary")[1, 1:5]),
c(NA, 0, 0, 0, 0))
expect_equal(as.vector(assay(cons_adj, "combine_ndotproduct")[15, 15:20]),
c(NA, "0.130802929034727", "", "", "", ""))
expect_equal(dim(assay(cons_adj, "combine_binary")), c(36, 36))
expect_equal(rownames(assay(cons_adj, "combine_ndotproduct")),
rownames(assay(spect_adj, "ndotproduct")))
expect_equal(colnames(assay(cons_adj, "combine_ndotproduct")),
colnames(assay(spect_adj, "ndotproduct")))
})
## END unit test spectral similarity ##
tnaake/MetNet documentation built on Nov. 4, 2024, 4:45 a.m.
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## create toy example data set
data("mat_test", package = "MetNet")
colnames(mat_test) <- paste0("intensity_", 1:20)
mz <- c(100, 150, 262.0528, 262.0528, 262.0528, 348.0532, 448.0532)
rt <- c(100, 100, 50, 150, 150, 150, 150)
mat_test <- cbind(mz = mz, rt = rt, mat_test)
rownames(mat_test) <- paste(mz, rt, sep = "_")
mat_test_old <- mat_test
# test the case when the transformation list is a tibble object
## transformations object for structural calculation
transformations <-
rbind(c("Malonyl group (-H2O)", "C3H2O3", 86.0003939305, "+"),
c("Monosaccharide (-H2O)", "C6H10O5", 162.0528234315, "-"))
transformations_neg <- transformations <-
tibble::as_tibble(data.frame(
group = transformations[, 1],
formula = transformations[, 2],
mass = as.numeric(transformations[, 3]),
rt = transformations[, 4]))
transformations_neg[, 3] <- -1 * transformations_neg[, 3]
## START unit test structural ##
struct_adj_old <- struct_adj <-
structural(
mat_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE
)
struct_adj_neg <-
structural(
mat_test, transformation = transformations_neg,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE
)
struct_adj_dir_old <- struct_adj_dir <-
structural(
mat_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE
)
struct_adj_dir_neg <-
structural(
mat_test, transformation = transformations_neg,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE
)
g_undir <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj, "binary", mode = "directed", weighted = NULL)
)
g_undir_neg <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_neg, "binary", mode = "directed", weighted = NULL)
)
g_dir <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir, "binary"), mode = "directed", weighted = NULL
)
g_dir_neg <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir_neg, "binary"), mode = "directed", weighted = NULL
)
plot(g_undir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_undir_neg, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir_neg, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
test_that("structural", {
expect_error(structural(mat_test[, -1], transformations),
"does not contain the column mz")
expect_error(structural(NULL, transformations),
"'x' has to be a matrix or data.frame")
expect_error(structural(mat_test, transformations[, -3]),
"does not contain the column mass")
expect_error(structural(mat_test, matrix()),
"is not a data.frame")
expect_error(structural(mat_test, transformations, ppm = "a"),
"'ppm' has to be a numeric of length 1")
expect_error(structural(mat_test, transformations, var = c("group", "foo")),
"'transformation' does not contain the column 'foo'")
expect_error(structural(mat_test, transformations, var = "foo"),
"'transformation' does not contain the column 'foo'")
expect_error(structural(mat_test, transformations,
var = c("group", "foo", "foo2")),
"'transformation' does not contain the column 'foo', 'foo2'")
expect_error(structural(mat_test, transformations, var = c("foo", "foo2")),
"'transformation' does not contain the column 'foo', 'foo2'")
expect_error(structural(mat_test, transformations, var = ""),
"'transformation' does not contain the column ''")
expect_error(structural(mat_test, transformations, var = NULL),
"'var' is not a character vector")
expect_error(structural(mat_test, transformations, var = numeric()),
"'var' is not a character vector")
expect_error(structural(mat_test, transformations, var = logical()),
"'var' is not a character vector")
expect_equal(assayNames(structural(mat_test, transformations,
var = character())), "binary")
expect_true(validObject(struct_adj))
expect_equal(assayNames(struct_adj), c("binary", "group", "formula", "mass"))
expect_equal(length(struct_adj), 7)
expect_equal(dim(struct_adj), c(7, 7))
expect_equal(dim(assay(struct_adj, "binary")), c(7, 7))
expect_equal(dim(assay(struct_adj, "group")), c(7, 7))
expect_equal(dim(assay(struct_adj, "formula")), c(7, 7))
expect_equal(dim(assay(struct_adj, "mass")), c(7, 7))
expect_equal(rownames(assay(struct_adj, 1)), colnames(assay(struct_adj, 1)))
expect_equal(rownames(assay(struct_adj, 2)), colnames(assay(struct_adj, 2)))
expect_equal(rownames(assay(struct_adj, 3)), rownames(assay(struct_adj, 3)))
expect_equal(rownames(assay(struct_adj, 4)), rownames(assay(struct_adj, 4)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 2)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 3)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 4)))
expect_equal(rownames(assay(struct_adj, 1)), paste(mz, rt, sep = "_"))
expect_equal(sum(assay(struct_adj, "binary")), 12)
expect_equal(sum(assay(struct_adj_neg, "binary")), 0)
expect_equal(sum(assay(struct_adj_dir, "binary")), 6)
expect_equal(sum(assay(struct_adj_dir_neg, "binary")), 6)
expect_equal(as.vector(assay(struct_adj, "group")[, 1]),
c("", "", "Monosaccharide (-H2O)", "Monosaccharide (-H2O)",
"Monosaccharide (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 3]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 4]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 5]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 6]),
c("", "", "Malonyl group (-H2O)", "Malonyl group (-H2O)",
"Malonyl group (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 1]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 3]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 4]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 5]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 6]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 1]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 3]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 4]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 5]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 6]),
c("", "", "Malonyl group (-H2O)", "Malonyl group (-H2O)",
"Malonyl group (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 1]),
c("", "", "Monosaccharide (-H2O)", "Monosaccharide (-H2O)",
"Monosaccharide (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 3]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 4]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 5]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 6]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(unique(as.vector(assay(struct_adj, "group"))),
c("", "Monosaccharide (-H2O)", "Malonyl group (-H2O)"))
expect_equal(unique(as.vector(assay(struct_adj, "mass"))),
c("", "162.0528234315", "86.0003939305"))
expect_equal(unique(as.vector(assay(struct_adj, "formula"))),
c("", "C6H10O5", "C3H2O3"))
expect_true(is.matrix(assay(struct_adj, "binary")))
expect_true(is.matrix(assay(struct_adj, "group")))
expect_true(is.matrix(assay(struct_adj, "mass")))
expect_true(is.matrix(assay(struct_adj, "formula")))
expect_true(is.numeric(assay(struct_adj, "binary")))
expect_true(is.character(assay(struct_adj, "group")))
expect_true(is.character(assay(struct_adj, "mass")))
expect_true(is.character(assay(struct_adj, "formula")))
expect_equal(struct_adj@directed, FALSE)
expect_equal(struct_adj_neg@directed, FALSE)
expect_equal(struct_adj_dir@directed, TRUE)
expect_equal(struct_adj_dir_neg@directed, TRUE)
expect_equal(struct_adj@type, "structural")
expect_equal(struct_adj_neg@type, "structural")
expect_equal(struct_adj_dir@type, "structural")
expect_equal(struct_adj_dir_neg@type, "structural")
expect_equal(struct_adj@thresholded, FALSE)
expect_equal(struct_adj_neg@thresholded, FALSE)
expect_equal(struct_adj_dir@thresholded, FALSE)
expect_equal(struct_adj_dir_neg@thresholded, FALSE)
## test for mass difference value of 0
mat_test <- mat_test_old
mat_test[,"mz"] <-
c(100, 150, 262.0528, 262.0528, 262.0528, 348.0532, 448.0532)
mat_test[, "rt"] <- c(100, 100, 50, 150, 151, 150, 150)
rownames(mat_test) <- paste(mat_test[, "mz"], mat_test[, "rt"], sep = "_")
transformations_0 <- data.frame(
group = "no transformation", formula = "", mass = 0, rt = "?")
struct_adj_dir <- structural(mat_test, transformation = transformations_0,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE)
struct_adj_undir <- structural(mat_test, transformation = transformations_0,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE)
a_dir <- assay(struct_adj_dir, "binary")
a_undir <- assay(struct_adj_undir, "binary")
expect_equal(sum(a_dir), 13)
expect_equal(as.vector(a_dir["100_100", ]), c(1, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["150_100", ]), c(0, 1, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["262.0528_50", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["262.0528_150", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["262.0528_151", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["348.0532_150", ]), c(0, 0, 0, 0, 0, 1, 0))
expect_equal(as.vector(a_dir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(sum(a_undir), 13)
expect_equal(as.vector(a_undir["100_100", ]), c(1, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["150_100", ]), c(0, 1, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["262.0528_50", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["262.0528_150", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["262.0528_151", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["348.0532_150", ]), c(0, 0, 0, 0, 0, 1, 0))
expect_equal(as.vector(a_undir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
## another test with transformation slighty > 0 and very small ppm
mat_test <- mat_test_old
mat_test[, "mz"] <- c(100, 150, 262.0528, 263.0528, 263.0538, 448.0532, 448.0542)
mat_test[, "rt"] <- c(100, 100, 50, 150, 151, 150, 150)
rownames(mat_test) <- paste(mat_test[, "mz"], mat_test[, "rt"], sep = "_")
transformations_1 <- data.frame(
group = "no transformation", formula = "", mass = 0.001,
rt = "?")
struct_adj_dir <- structural(mat_test, transformation = transformations_1,
var = c("group", "formula", "mass"), ppm = 1, directed = TRUE)
struct_adj_undir <- structural(mat_test, transformation = transformations_1,
var = c("group", "formula", "mass"), ppm = 1, directed = FALSE)
a_dir <- assay(struct_adj_dir, "binary")
a_undir <- assay(struct_adj_undir, "binary")
expect_equal(sum(a_dir), 2)
expect_equal(as.vector(a_dir["100_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["150_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["262.0528_50", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["263.0528_150", ]), c(0, 0, 0, 0, 1, 0, 0))
expect_equal(as.vector(a_dir["263.0538_151", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(as.vector(a_dir["448.0542_150", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(sum(a_undir), 4)
expect_equal(as.vector(a_undir["100_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["150_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["262.0528_50", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["263.0528_150", ]), c(0, 0, 0, 0, 1, 0, 0))
expect_equal(as.vector(a_undir["263.0538_151", ]), c(0, 0, 0, 1, 0, 0, 0))
expect_equal(as.vector(a_undir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(as.vector(a_undir["448.0542_150", ]), c(0, 0, 0, 0, 0, 1, 0))
})
## transformations object for structural calculation
transformations <- rbind(
c("Malonyl group (-H2O)", "C3H2O3", 86.0003939305, "+"),
c("Monosaccharide (-H2O)", "C6H10O5", 162.0528234315, "-"))
transformations_neg <- transformations_old <- transformations <- data.frame(
group = transformations[, 1],
formula = transformations[, 2],
mass = as.numeric(transformations[, 3]),
rt = transformations[, 4])
transformations_neg[, 3] <- -1 * transformations_neg[, 3]
## START unit test structural ##
struct_adj_old <- struct_adj <- structural(mat_test,
transformation = transformations, var = c("group", "formula", "mass"),
ppm = 5, directed = FALSE)
struct_adj_neg <- structural(mat_test, transformation = transformations_neg,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE)
struct_adj_dir_old <- struct_adj_dir <- structural(mat_test,
transformation = transformations, var = c("group", "formula", "mass"),
ppm = 5, directed = TRUE)
struct_adj_dir_neg <- structural(mat_test, transformation = transformations_neg,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE)
g_undir <- igraph::graph_from_adjacency_matrix(
assay(struct_adj, "binary", mode = "directed", weighted = NULL))
g_undir_neg <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_neg, "binary", mode = "directed", weighted = NULL))
g_dir <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir, "binary"), mode = "directed", weighted = NULL)
g_dir_neg <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir_neg, "binary"), mode = "directed", weighted = NULL)
plot(g_undir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_undir_neg, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir_neg, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
test_that("structural", {
expect_error(structural(mat_test[, -1], transformations),
"does not contain the column mz")
expect_error(structural(NULL, transformations),
"'x' has to be a matrix or data.frame")
expect_error(structural(mat_test, transformations[, -3]),
"does not contain the column mass")
expect_error(structural(mat_test, matrix()),
"is not a data.frame")
expect_error(structural(mat_test, transformations, ppm = "a"),
"'ppm' has to be a numeric of length 1")
expect_error(structural(mat_test, transformations, var = c("group", "foo")),
"'transformation' does not contain the column 'foo'")
expect_error(structural(mat_test, transformations, var = "foo"),
"'transformation' does not contain the column 'foo'")
expect_error(structural(mat_test, transformations,
var = c("group", "foo", "foo2")),
"'transformation' does not contain the column 'foo', 'foo2'")
expect_error(structural(mat_test, transformations,
var = c("foo", "foo2")),
"'transformation' does not contain the column 'foo', 'foo2'")
expect_error(structural(mat_test, transformations, var = ""),
"'transformation' does not contain the column ''")
expect_error(structural(mat_test, transformations, var = NULL),
"'var' is not a character vector")
expect_error(structural(mat_test, transformations, var = numeric()),
"'var' is not a character vector")
expect_error(structural(mat_test, transformations, var = logical()),
"'var' is not a character vector")
expect_equal(assayNames(structural(mat_test, transformations,
var = character())), "binary")
expect_true(validObject(struct_adj))
expect_equal(assayNames(struct_adj),
c("binary", "group", "formula", "mass"))
expect_equal(length(struct_adj), 7)
expect_equal(dim(struct_adj), c(7, 7))
expect_equal(dim(assay(struct_adj, "binary")), c(7, 7))
expect_equal(dim(assay(struct_adj, "group")), c(7, 7))
expect_equal(dim(assay(struct_adj, "formula")), c(7, 7))
expect_equal(dim(assay(struct_adj, "mass")), c(7, 7))
expect_equal(rownames(assay(struct_adj, 1)), colnames(assay(struct_adj, 1)))
expect_equal(rownames(assay(struct_adj, 2)), colnames(assay(struct_adj, 2)))
expect_equal(rownames(assay(struct_adj, 3)), rownames(assay(struct_adj, 3)))
expect_equal(rownames(assay(struct_adj, 4)), rownames(assay(struct_adj, 4)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 2)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 3)))
expect_equal(rownames(assay(struct_adj, 1)), rownames(assay(struct_adj, 4)))
expect_equal(rownames(assay(struct_adj, 1)), paste(mz, rt, sep = "_"))
expect_equal(sum(assay(struct_adj, "binary")), 12)
expect_equal(sum(assay(struct_adj_neg, "binary")), 0)
expect_equal(sum(assay(struct_adj_dir, "binary")), 6)
expect_equal(sum(assay(struct_adj_dir_neg, "binary")), 6)
expect_equal(as.vector(assay(struct_adj, "group")[, 1]),
c("", "", "Monosaccharide (-H2O)", "Monosaccharide (-H2O)",
"Monosaccharide (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 3]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 4]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 5]),
c("Monosaccharide (-H2O)", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 6]),
c("", "", "Malonyl group (-H2O)", "Malonyl group (-H2O)",
"Malonyl group (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 1]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 3]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 4]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 5]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 6]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_neg, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 1]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 3]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 4]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 5]),
c("Monosaccharide (-H2O)", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 6]),
c("", "", "Malonyl group (-H2O)", "Malonyl group (-H2O)",
"Malonyl group (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj_dir, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 1]),
c("", "", "Monosaccharide (-H2O)", "Monosaccharide (-H2O)",
"Monosaccharide (-H2O)", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 2]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 3]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 4]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 5]),
c("", "", "", "", "", "Malonyl group (-H2O)", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 6]),
c("", "", "", "", "", "", ""))
expect_equal(as.vector(assay(struct_adj_dir_neg, "group")[, 7]),
c("", "", "", "", "", "", ""))
expect_equal(unique(as.vector(assay(struct_adj, "group"))),
c("", "Monosaccharide (-H2O)", "Malonyl group (-H2O)"))
expect_equal(unique(as.vector(assay(struct_adj, "mass"))),
c("", "162.0528234315", "86.0003939305"))
expect_equal(unique(as.vector(assay(struct_adj, "formula"))),
c("", "C6H10O5", "C3H2O3"))
expect_true(is.matrix(assay(struct_adj, "binary")))
expect_true(is.matrix(assay(struct_adj, "group")))
expect_true(is.matrix(assay(struct_adj, "mass")))
expect_true(is.matrix(assay(struct_adj, "formula")))
expect_true(is.numeric(assay(struct_adj, "binary")))
expect_true(is.character(assay(struct_adj, "group")))
expect_true(is.character(assay(struct_adj, "mass")))
expect_true(is.character(assay(struct_adj, "formula")))
expect_equal(struct_adj@directed, FALSE)
expect_equal(struct_adj_neg@directed, FALSE)
expect_equal(struct_adj_dir@directed, TRUE)
expect_equal(struct_adj_dir_neg@directed, TRUE)
expect_equal(struct_adj@type, "structural")
expect_equal(struct_adj_neg@type, "structural")
expect_equal(struct_adj_dir@type, "structural")
expect_equal(struct_adj_dir_neg@type, "structural")
expect_equal(struct_adj@thresholded, FALSE)
expect_equal(struct_adj_neg@thresholded, FALSE)
expect_equal(struct_adj_dir@thresholded, FALSE)
expect_equal(struct_adj_dir_neg@thresholded, FALSE)
## test for mass difference value of 0
mat_test <- mat_test_old
mat_test[,"mz"] <- c(100, 150, 262.0528, 262.0528, 262.0528, 348.0532, 448.0532)
mat_test[, "rt"] <- c(100, 100, 50, 150, 151, 150, 150)
rownames(mat_test) <- paste(mat_test[, "mz"], mat_test[, "rt"], sep = "_")
transformations_0 <- data.frame(
group = "no transformation", formula = "", mass = 0, rt = "?")
struct_adj_dir <- structural(mat_test, transformation = transformations_0,
var = c("group", "formula", "mass"), ppm = 5, directed = TRUE)
struct_adj_undir <- structural(mat_test, transformation = transformations_0,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE)
a_dir <- assay(struct_adj_dir, "binary")
a_undir <- assay(struct_adj_undir, "binary")
expect_equal(sum(a_dir), 13)
expect_equal(as.vector(a_dir["100_100", ]), c(1, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["150_100", ]), c(0, 1, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["262.0528_50", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["262.0528_150", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["262.0528_151", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_dir["348.0532_150", ]), c(0, 0, 0, 0, 0, 1, 0))
expect_equal(as.vector(a_dir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(sum(a_undir), 13)
expect_equal(as.vector(a_undir["100_100", ]), c(1, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["150_100", ]), c(0, 1, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["262.0528_50", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["262.0528_150", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["262.0528_151", ]), c(0, 0, 1, 1, 1, 0, 0))
expect_equal(as.vector(a_undir["348.0532_150", ]), c(0, 0, 0, 0, 0, 1, 0))
expect_equal(as.vector(a_undir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
## another test with transformation slighty > 0 and very small ppm
mat_test <- mat_test_old
mat_test[, "mz"] <- c(100, 150, 262.0528, 263.0528, 263.0538, 448.0532, 448.0542)
mat_test[, "rt"] <- c(100, 100, 50, 150, 151, 150, 150)
rownames(mat_test) <- paste(mat_test[, "mz"], mat_test[, "rt"], sep = "_")
transformations_1 <- data.frame(
group = "no transformation", formula = "", mass = 0.001,
rt = "?")
struct_adj_dir <- structural(mat_test, transformation = transformations_1,
var = c("group", "formula", "mass"), ppm = 1, directed = TRUE)
struct_adj_undir <- structural(mat_test, transformation = transformations_1,
var = c("group", "formula", "mass"), ppm = 1, directed = FALSE)
a_dir <- assay(struct_adj_dir, "binary")
a_undir <- assay(struct_adj_undir, "binary")
expect_equal(sum(a_dir), 2)
expect_equal(as.vector(a_dir["100_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["150_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["262.0528_50", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["263.0528_150", ]), c(0, 0, 0, 0, 1, 0, 0))
expect_equal(as.vector(a_dir["263.0538_151", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_dir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(as.vector(a_dir["448.0542_150", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(sum(a_undir), 4)
expect_equal(as.vector(a_undir["100_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["150_100", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["262.0528_50", ]), c(0, 0, 0, 0, 0, 0, 0))
expect_equal(as.vector(a_undir["263.0528_150", ]), c(0, 0, 0, 0, 1, 0, 0))
expect_equal(as.vector(a_undir["263.0538_151", ]), c(0, 0, 0, 1, 0, 0, 0))
expect_equal(as.vector(a_undir["448.0532_150", ]), c(0, 0, 0, 0, 0, 0, 1))
expect_equal(as.vector(a_undir["448.0542_150", ]), c(0, 0, 0, 0, 0, 1, 0))
})
## END unit test structural ##
## START unit test rtCorrection ##
struct_adj <- struct_adj_old
struct_adj_dir <- struct_adj_dir_old
mat_test <- mat_test_old
transformations <- transformations_old
struct_adj_rt <- rtCorrection(struct_adj, mat_test, transformations,
var = "group")
struct_adj_rt_dir <- rtCorrection(struct_adj_dir, mat_test, transformations,
var = "group")
g_undir <- igraph::graph_from_adjacency_matrix(
assay(struct_adj, "binary", mode = "directed", weighted = NULL))
g_undir_rt <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_rt, "binary", mode = "directed", weighted = NULL))
g_dir <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir, "binary"), mode = "directed", weighted = NULL)
g_dir_rt <- igraph::graph_from_adjacency_matrix(
assay(struct_adj_rt_dir, "binary"), mode = "directed", weighted = NULL)
plot(g_undir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_undir_rt, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
plot(g_dir_rt, edge.width = 1, edge.arrow.size = 0.5,
vertex.label.cex = 0.8, edge.color = "grey")
test_that("rtCorrection", {
expect_error(rtCorrection(struct_adj[[1]], mat_test, transformations),
"is not an 'AdjacencyMatrix'")
tmp <- struct_adj
assay(tmp, "transformation") <- assay(tmp, "binary")
expect_error(rtCorrection(tmp, mat_test, transformations),
"must be character")
tmp <- struct_adj
assay(tmp, "mass") <- assay(tmp, "binary")
expect_error(rtCorrection(tmp, mat_test, transformations),
"must be character")
expect_error(rtCorrection(struct_adj, NULL, transformations),
"'x' does not contain the column 'rt'")
expect_error(rtCorrection(struct_adj, mat_test[, -1], transformations),
"'x' does not contain the column 'mz'")
expect_error(rtCorrection(struct_adj, mat_test[, -2], transformations),
"'x' does not contain the column 'rt'")
expect_error(rtCorrection(struct_adj, mat_test, NULL),
"'transformation' does not contain the column 'group'")
expect_error(rtCorrection(struct_adj, mat_test, transformations[, -1]),
"'transformation' does not contain the column 'group'")
expect_error(rtCorrection(struct_adj, mat_test, transformations[, -4]),
"'transformation' does not contain the column 'rt'")
expect_error(rtCorrection(struct_adj, mat_test,
transformation = cbind(transformations[, -4], rt = rep("a", 2))),
"does contain other")
expect_true(is.matrix(assay(struct_adj_rt, "binary")))
expect_true(is.numeric(assay(struct_adj_rt, "binary")))
expect_true(is.matrix(assay(struct_adj_rt, "group")))
expect_true(is.character(assay(struct_adj_rt, "group")))
expect_true(is.matrix(assay(struct_adj_rt, "mass")))
expect_true(is.character(assay(struct_adj_rt, "mass")))
expect_true(is.matrix(assay(struct_adj_rt, "formula")))
expect_true(is.character(assay(struct_adj_rt, "formula")))
expect_equal(colnames(assay(struct_adj_rt, "binary")),
paste(mz, rt, sep = "_"))
expect_equal(colnames(assay(struct_adj_rt, 1)),
rownames(assay(struct_adj_rt, 1)))
expect_equal(colnames(assay(struct_adj_rt, 2)),
rownames(assay(struct_adj_rt, 2)))
expect_equal(colnames(assay(struct_adj_rt, 3)),
rownames(assay(struct_adj_rt, 3)))
expect_equal(colnames(assay(struct_adj_rt, 1)),
colnames(assay(struct_adj_rt, 2)))
expect_equal(colnames(assay(struct_adj_rt, 1)),
colnames(assay(struct_adj_rt, 3)))
expect_true(table(assay(struct_adj_rt, "binary"))[1] == 41)
expect_true(table(assay(struct_adj_rt_dir, "binary"))[1] == 45)
expect_equal(sum(assay(struct_adj_rt, "binary")), 8)
expect_equal(sum(assay(struct_adj_rt_dir, "binary")), 4)
expect_true(all(
table(assay(struct_adj_rt, "group")) == c(41, 6, 2)))
expect_true(all(
table(assay(struct_adj_rt, "mass")) == c(41, 2, 6)))
expect_true(all(
table(assay(struct_adj_rt, "formula")) == c(41, 6, 2)))
expect_true(all(
table(assay(struct_adj_rt_dir, "group")) == c(45, 3, 1)))
expect_true(all(
table(assay(struct_adj_rt_dir, "mass")) == c(45, 1, 3)))
expect_true(all(
table(assay(struct_adj_rt_dir, "formula")) == c(45, 3, 1)))
expect_equal(directed(struct_adj_rt), FALSE)
expect_equal(directed(struct_adj_rt_dir), TRUE)
expect_equal(type(struct_adj_rt), "structural")
expect_equal(type(struct_adj_rt_dir), "structural")
expect_equal(thresholded(struct_adj_rt), TRUE)
expect_equal(thresholded(struct_adj_rt_dir), TRUE)
## create a double assignment to certain cells
transformations <- rbind(transformations,
data.frame(group = "pseudo Monosaccharide",
formula = "C6H10O5", mass = 162.05282, rt = "?"))
struct_adj_pseudo <- structural(mat_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE)
expect_equal(assay(struct_adj_pseudo, "group")[3, 1],
"Monosaccharide (-H2O)/pseudo Monosaccharide")
expect_equal(assay(struct_adj_pseudo, "mass")[3, 1],
"162.0528234315/162.05282")
expect_equal(assay(struct_adj_pseudo, "formula")[3, 1],
"C6H10O5/C6H10O5")
struct_adj_pseudo_rt <- rtCorrection(struct_adj_pseudo, x = mat_test,
transformation = transformations, var = "group")
})
## test rtCorrection with the transformation table as tibble
struct_adj <- struct_adj_old
struct_adj_dir <- struct_adj_dir_old
mat_test <- mat_test_old
transformations <- tibble::as_tibble(transformations_old)
struct_adj_rt <-
rtCorrection(struct_adj, mat_test, transformations, var = "group")
struct_adj_rt_dir <-
rtCorrection(struct_adj_dir, mat_test, transformations, var = "group")
g_undir <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj, "binary", mode = "directed", weighted = NULL)
)
g_undir_rt <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_rt, "binary", mode = "directed", weighted = NULL)
)
g_dir <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_dir, "binary"), mode = "directed", weighted = NULL
)
g_dir_rt <-
igraph::graph_from_adjacency_matrix(
assay(struct_adj_rt_dir, "binary"), mode = "directed", weighted = NULL
)
plot(
g_undir, edge.width = 1, edge.arrow.size = 0.5, vertex.label.cex = 0.8,
edge.color = "grey"
)
plot(
g_undir_rt, edge.width = 1, edge.arrow.size = 0.5, vertex.label.cex = 0.8,
edge.color = "grey"
)
plot(
g_dir, edge.width = 1, edge.arrow.size = 0.5, vertex.label.cex = 0.8,
edge.color = "grey"
)
plot(
g_dir_rt, edge.width = 1, edge.arrow.size = 0.5, vertex.label.cex = 0.8,
edge.color = "grey"
)
test_that("rtCorrection", {
expect_error(
rtCorrection(struct_adj[[1]], mat_test, transformations),
"is not an 'AdjacencyMatrix'"
)
tmp <- struct_adj
assay(tmp, "transformation") <- assay(tmp, "binary")
expect_error(
rtCorrection(tmp, mat_test, transformations), "must be character"
)
tmp <- struct_adj
assay(tmp, "mass") <- assay(tmp, "binary")
expect_error(
rtCorrection(tmp, mat_test, transformations), "must be character"
)
expect_error(
rtCorrection(struct_adj, NULL, transformations),
"'x' does not contain the column 'rt'"
)
expect_error(
rtCorrection(struct_adj, mat_test[, -1], transformations),
"'x' does not contain the column 'mz'"
)
expect_error(
rtCorrection(struct_adj, mat_test[, -2], transformations),
"'x' does not contain the column 'rt'"
)
expect_error(
rtCorrection(struct_adj, mat_test, NULL),
"'transformation' does not contain the column 'group'"
)
expect_error(
rtCorrection(struct_adj, mat_test, transformations[, -1]),
"'transformation' does not contain the column 'group'"
)
expect_error(
rtCorrection(struct_adj, mat_test, transformations[, -4]),
"'transformation' does not contain the column 'rt'"
)
expect_error(
rtCorrection(
struct_adj, mat_test,
transformation = cbind(transformations[, -4], rt = rep("a", 2))
), "does contain other"
)
expect_true(is.matrix(assay(struct_adj_rt, "binary")))
expect_true(is.numeric(assay(struct_adj_rt, "binary")))
expect_true(is.matrix(assay(struct_adj_rt, "group")))
expect_true(is.character(assay(struct_adj_rt, "group")))
expect_true(is.matrix(assay(struct_adj_rt, "mass")))
expect_true(is.character(assay(struct_adj_rt, "mass")))
expect_true(is.matrix(assay(struct_adj_rt, "formula")))
expect_true(is.character(assay(struct_adj_rt, "formula")))
expect_equal(
colnames(assay(struct_adj_rt, "binary")), paste(mz, rt, sep = "_")
)
expect_equal(
colnames(assay(struct_adj_rt, 1)), rownames(assay(struct_adj_rt, 1))
)
expect_equal(
colnames(assay(struct_adj_rt, 2)), rownames(assay(struct_adj_rt, 2))
)
expect_equal(
colnames(assay(struct_adj_rt, 3)), rownames(assay(struct_adj_rt, 3))
)
expect_equal(
colnames(assay(struct_adj_rt, 1)), colnames(assay(struct_adj_rt, 2))
)
expect_equal(
colnames(assay(struct_adj_rt, 1)), colnames(assay(struct_adj_rt, 3))
)
expect_true(table(assay(struct_adj_rt, "binary"))[1] == 41)
expect_true(table(assay(struct_adj_rt_dir, "binary"))[1] == 45)
expect_equal(sum(assay(struct_adj_rt, "binary")), 8)
expect_equal(sum(assay(struct_adj_rt_dir, "binary")), 4)
expect_true(all(table(assay(struct_adj_rt, "group")) == c(41, 6, 2)))
expect_true(all(table(assay(struct_adj_rt, "mass")) == c(41, 2, 6)))
expect_true(all(table(assay(struct_adj_rt, "formula")) == c(41, 6, 2)))
expect_true(all(table(assay(struct_adj_rt_dir, "group")) == c(45, 3, 1)))
expect_true(all(table(assay(struct_adj_rt_dir, "mass")) == c(45, 1, 3)))
expect_true(all(table(assay(struct_adj_rt_dir, "formula")) == c(45, 3, 1)))
expect_equal(directed(struct_adj_rt), FALSE)
expect_equal(directed(struct_adj_rt_dir), TRUE)
expect_equal(type(struct_adj_rt), "structural")
expect_equal(type(struct_adj_rt_dir), "structural")
expect_equal(thresholded(struct_adj_rt), TRUE)
expect_equal(thresholded(struct_adj_rt_dir), TRUE)
## create a double assignment to certain cells
transformations <-
rbind(
transformations,
data.frame(
group = "pseudo Monosaccharide", formula = "C6H10O5", mass = 162.05282,
rt = "?"
)
)
struct_adj_pseudo <-
structural(
mat_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5, directed = FALSE
)
expect_equal(
assay(struct_adj_pseudo, "group")[3, 1],
"Monosaccharide (-H2O)/pseudo Monosaccharide"
)
expect_equal(
assay(struct_adj_pseudo, "mass")[3, 1], "162.0528234315/162.05282"
)
expect_equal(assay(struct_adj_pseudo, "formula")[3, 1], "C6H10O5/C6H10O5")
struct_adj_pseudo_rt <-
rtCorrection(
struct_adj_pseudo, x = mat_test, transformation = transformations,
var = "group"
)
})
## END unit test rtCorrection ##
## create toy example data set
data("x_test", package = "MetNet")
x_test <- as.matrix(x_test)
## transformations object for structural calculation
transformations <- rbind(
c("Malonyl group (-H2O)", "C3H2O3", "86.0003939305"),
c("Monosaccharide (-H2O)", "C6H10O5", "162.0528234315"))
transformations <- data.frame(group = as.character(transformations[, 1]),
formula = as.character(transformations[, 2]),
mass = as.numeric(transformations[, 3]))
## create structural network
struct_adj <- structural(x_test, transformation = transformations,
var = c("group", "formula", "mass"), ppm = 5)
## create statistical network
stat_adj <- statistical(x_test[, -c(1:2)],
model = c("clr", "aracne", "pearson", "spearman", "ggm"))
stat_adj_thr <- threshold(stat_adj, type = "top2", args = list(n = 10))
## load MS2
f <- system.file("spectra_matrix/spectra_matrix.RDS", package = "MetNet")
adj_spec <- readRDS(f)
## START unit test spectral similarity ##
spect_adj <- addSpectralSimilarity(am_structural = struct_adj,
ms2_similarity = list("ndotproduct" = adj_spec))
test_that("addSpectralSimilarity", {
expect_error(addSpectralSimilarity(adj_spec, NULL),
"'am_structural' is not an 'AdjacencyMatrix' object")
expect_true(validObject(spect_adj))
expect_equal(assayNames(spect_adj),
c("binary", "group", "formula", "mass", "ndotproduct"))
expect_equal(sum(assay(spect_adj, "ndotproduct"), na.rm = TRUE),
45.16721, tolerance = 5e-01)
expect_equal(as.vector(assay(spect_adj, "ndotproduct")[7, 1:10]),
c(0, 0, 0, 0.989282368, 0, 0, 1, 0.003863543, 0, 0))
expect_equal(rownames(assay(spect_adj, "ndotproduct")),
colnames(assay(spect_adj, "ndotproduct")))
expect_equal(rownames(assay(spect_adj, "ndotproduct")),
colnames(assay(struct_adj, "binary")))
expect_true(is.numeric(assay(spect_adj, "ndotproduct")))
})
## test threshold() and combine()
args_thr <- list(filter = "ndotproduct > 0.1 |
binary == 1 & is.na(ndotproduct)")
thr_thr <- threshold(spect_adj, type = "threshold", args = args_thr)
cons_adj <- combine(thr_thr, stat_adj_thr)
test_that("threshold and combine similarity", {
expect_error(threshold(spect_adj, type = "top1", args = list(n = 2)),
"'am' 'structural' can only be thresholded by 'type = threshold'")
expect_true(is(thr_thr, "AdjacencyMatrix"))
expect_equal(assayNames(thr_thr),
c("binary", "group", "formula", "mass", "ndotproduct"))
expect_true(is.numeric(assay(thr_thr, "binary")))
expect_equal(rownames(assay(thr_thr, "binary")),
rownames(assay(spect_adj, "binary")))
expect_equal(colnames(assay(thr_thr, "binary")),
colnames(assay(spect_adj, "binary")))
expect_equal(sum(assay(thr_thr, "binary"), na.rm = TRUE), 60)
expect_true(all(assay(thr_thr, "binary") %in% c(0, 1, NaN)))
## test combine
expect_true(validObject(cons_adj))
expect_equal(assayNames(cons_adj),
c("binary", "group", "formula", "mass", "ndotproduct",
"clr_coef", "aracne_coef", "pearson_coef", "pearson_pvalue",
"spearman_coef", "spearman_pvalue", "ggm_coef", "ggm_pvalue",
"consensus", "combine_binary", "combine_group",
"combine_formula", "combine_mass", "combine_ndotproduct"))
expect_equal(sum(assay(cons_adj, "combine_binary"), na.rm = TRUE), 4)
expect_equal(as.vector(assay(cons_adj, "combine_binary")[1, 1:5]),
c(NA, 0, 0, 0, 0))
expect_equal(as.vector(assay(cons_adj, "combine_ndotproduct")[15, 15:20]),
c(NA, "0.130802929034727", "", "", "", ""))
expect_equal(dim(assay(cons_adj, "combine_binary")), c(36, 36))
expect_equal(rownames(assay(cons_adj, "combine_ndotproduct")),
rownames(assay(spect_adj, "ndotproduct")))
expect_equal(colnames(assay(cons_adj, "combine_ndotproduct")),
colnames(assay(spect_adj, "ndotproduct")))
})
## END unit test spectral similarity ##
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