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test-MultiAssayExperiment.R
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test-MultiAssayExperiment.R
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test_that("MultiAssayExperiment constructor works", {
obs <- MultiAssayExperiment()
expect_true(validObject(obs))
expect_identical(names(experiments(obs)), character())
expect_identical(length(experiments(obs)), 0L)
expect_identical(dim(sampleMap(obs)), c(0L, 3L))
expect_identical(dim(colData(obs)), c(0L, 0L))
expect_error(MultiAssayExperiment(list(matrix(0, 0, 0))),
label="unnamed ExperimentList")
obs <- MultiAssayExperiment(list(m=matrix(0, 0, 0)))
expect_true(validObject(obs))
expect_identical(names(experiments(obs)), "m")
expect_identical(length(experiments(obs)), 1L)
expect_identical(dim(sampleMap(obs)), c(0L, 3L))
expect_identical(dim(colData(obs)), c(0L, 0L))
colData <- S4Vectors::DataFrame(row.names=letters[1:4])
obs <- MultiAssayExperiment(colData=colData)
expect_true(validObject(obs))
expect_identical(names(experiments(obs)), character())
expect_identical(length(experiments(obs)), 0L)
expect_identical(dim(sampleMap(obs)), c(0L, 3L))
expect_identical(dim(colData(obs)), c(0L, 0L))
sampleMap <- S4Vectors::DataFrame(assay=factor("m", levels="m"),
primary=letters, colname=letters)
obs <- MultiAssayExperiment(sampleMap=sampleMap)
expect_true(validObject(obs))
expect_identical(nrow(sampleMap(obs)), 0L)
expect_identical(length(experiments(obs)), 0L)
expect_identical(dim(colData(obs)), c(0L, 0L))
# test multiple experiment
m <- matrix(0, 3, 3, dimnames=list(letters[1:3], letters[1:3]))
m2 <- matrix(0, 0, 0)
m3 <- matrix(0, 1, 1, dimnames=list("d", "d"))
obs <- MultiAssayExperiment(list(m=m, m2=m2, m3=m3))
expect_true(validObject(obs))
expect_identical(length(experiments(obs)), 3L)
expect_identical(levels(sampleMap(obs)[["assay"]]), c("m", "m2", "m3"))
expect_identical(dim(sampleMap(obs)), c(4L, 3L))
expect_identical(rownames(colData(obs)), sampleMap(obs)[["primary"]])
})
test_that("MultiAssayExperiment .harmonize construction helper works", {
# remove unused assays in experiments not in sampleMap
m <- matrix(0, 2, 2, dimnames=list(letters[1:2], letters[1:2]))
experiments <- ExperimentList(list(m=m))
sampleMap <- S4Vectors::DataFrame(assay=factor("m", levels="m"),
primary="a", colname="a")
obs <- MultiAssayExperiment(experiments, sampleMap=sampleMap)
expect_identical(colnames(obs)[[1]], "a")
expect_identical(sampleMap(obs), sampleMap)
expect_identical(row.names(colData(obs)), "a")
# removed unused assays in sampleMap
sampleMap <- S4Vectors::DataFrame(assay=factor("m", levels="m"),
primary=letters, colname=letters)
obs <- MultiAssayExperiment(experiments, sampleMap=sampleMap)
expect_identical(colnames(experiments)[[1]], sampleMap(obs)[["colname"]])
expect_identical(experiments(obs), experiments)
expect_identical(colnames(experiments)[[1]], rownames(colData(obs)))
expect_identical(rownames(colData(obs)), sampleMap(obs)[["primary"]])
# colData subset by sampleData primary
colData <- S4Vectors::DataFrame(matrix(0, 4, 4, dimnames=list(letters[1:4],
letters[1:4])))
obs <- MultiAssayExperiment(experiments, sampleMap=sampleMap, colData=colData)
expect_identical(rownames(colData(obs)), sampleMap(obs)[["primary"]])
# combo subset
sampleMap <- S4Vectors::DataFrame(
assay=factor(c("m", "stack"), levels=c("m", "stack")),
primary=c("a", "n"),
colname=c("a", "n"))
m <- matrix(0, 3, 3, dimnames=list(letters[1:3], letters[1:3]))
colData <- S4Vectors::DataFrame(matrix(0, 4, 4, dimnames=list(letters[1:4],
letters[1:4])))
experiments <- ExperimentList(list(m=m))
obs <- MultiAssayExperiment(experiments=experiments,
sampleMap=sampleMap, colData=colData)
expect_identical(colnames(obs)[[1]], "a")
expect_identical(dim(sampleMap(obs)), c(1L, 3L))
expect_identical(rownames(colData(obs)), sampleMap(obs)[["primary"]])
# test multiple experiment, combo subsetting
m <- matrix(0, 3, 3, dimnames=list(letters[1:3], letters[1:3]))
m2 <- matrix(0, 0, 0)
m3 <- matrix(0, 2, 2, dimnames=list(letters[4:5], letters[4:5]))
experiments <- ExperimentList(list(m=m, m2=m2, m3=m3))
sampleMap <- S4Vectors::DataFrame(
assay=factor(c("m", "stack", "m3"), levels=c("m", "stack", "m3")),
primary=c("a", "n", "d"),
colname=c("a", "n", "d"))
colData <- S4Vectors::DataFrame(matrix(0, 7, 7,
dimnames=list(letters[1:7],
letters[1:7])))
obs <- MultiAssayExperiment(experiments=experiments,
sampleMap=sampleMap,
colData=colData)
expect_true(validObject(obs))
expect_identical(length(experiments(obs)), 2L)
expect_identical(dim(experiments(obs)[[1]]), c(3L, 1L))
expect_identical(dim(experiments(obs)[[2]]), c(2L, 1L))
expect_identical(names(experiments(obs)), c("m", "m3"))
expect_identical(dim(sampleMap(obs)), c(2L, 3L))
expect_identical(levels(sampleMap(obs)[["assay"]]), c("m", "m3"))
expect_identical(rownames(colData(obs)), sampleMap(obs)[["primary"]])
expect_identical(unlist(colnames(experiments(obs)), use.names=FALSE),
row.names(colData(obs)))
})
test_that("dropping experiments is noisy and traced", {
m <- matrix(0, 3, 3, dimnames=list(letters[1:3], letters[1:3]))
m2 <- matrix(0, 0, 0)
m3 <- matrix(0, 1, 1, dimnames=list("d", "d"))
mae <- MultiAssayExperiment(list(m=m, m2=m2, m3=m3))
## check warning about experiments
expect_warning( dp <- mae[, list(m = 1:3, m2 = 0, m3 = 1), , drop = TRUE] )
## check drops in mae
expect_identical(drops(dp)[["experiments"]], "m2")
## check warning about experiments
expect_warning( dp <- mae[character(0L), , drop = TRUE] )
## check drops in metadata
expect_identical(drops(dp)[["experiments"]], names(mae))
## check warning about experiments
expect_warning( dp <- mae[, , 0, drop = TRUE] )
## check drops in metadata
expect_identical(drops(dp)[["experiments"]], names(mae))
## check warning about experiments
expect_warning( dp <- mae[, , c(TRUE, FALSE), drop = TRUE] )
## check drops in metadata
expect_identical(drops(dp)[["experiments"]], "m2")
})
test_that("MultiAssayExperiment replacements work", {
pDF <- DataFrame(a = 1:4, b = letters[1:4])
obs <- MultiAssayExperiment()
expect_error(colData(obs) <- pDF)
})
test_that("MultiAssayExperiment name replacements work", {
m <- matrix(0, 3, 3, dimnames=list(letters[1:3], letters[1:3]))
m2 <- matrix(0, 0, 0)
m3 <- matrix(0, 1, 1, dimnames=list("d", "d"))
obs <- MultiAssayExperiment(list(m=m, m2=m2, m3=m3))
newnames <- c("exp1", "exp2", "exp3")
names(obs) <- newnames
expect_identical(names(obs), newnames)
expect_identical(levels(sampleMap(obs)[["assay"]]), newnames)
})
test_that("ExperimentList metadata and mcols are preserved", {
mcoldf <- DataFrame(AssayNumber=seq_len(length(ExpList)),
row.names = names(ExpList))
mcols(ExpList) <- mcoldf
metalist <- list(Shiny = "Blue Jeans", Old = "Metadata")
metadata(ExpList) <- metalist
mae0 <- MultiAssayExperiment(ExpList)
expect_identical(mcols(experiments(mae0)), mcoldf)
expect_identical(metadata(experiments(mae0)), metalist)
})
test_that("sampleMap is checked in MultiAssayExperiment constructor", {
se <- matrix(runif(100), 10, 10)
## empty sampleMap
expect_error(
MultiAssayExperiment(list(foo=se))
)
se <- matrix(runif(12), 3, 4, dimnames = list(letters[1:3], NULL))
asamp <- DataFrame(a = "a", b = "b", c = "c")
## sampleMap is missing required columns
expect_error(
MultiAssayExperiment(list(foo=se), sampleMap = asamp)
)
asamp <- DataFrame(
primary = "patA", assay = factor("foo"), colname = LETTERS[1:2]
)
expect_identical(
.checkFixSampleMap(asamp),
DataFrame(
assay = factor("foo"), primary = "patA", colname = LETTERS[1:2]
)
)
})
test_that("sampleMap is checked in MultiAssayExperiment validator", {
se <- matrix(runif(12), 3, 4, dimnames = list(letters[1:3], NULL))
asamp <- DataFrame(assay = factor("foo"), primary = "p1", colname = "col1")
## ExperimentList must be same length / ExperimentList names in sampleMap
expect_error(
new(
"MultiAssayExperiment",
ExperimentList = ExperimentList(list(foo = se, bar = se)),
sampleMap = asamp
)
)
se <- matrix(runif(100), 10, 10)
## All non-empty ExperimentList elements must be documented in sampleMap
expect_error(
new(
"MultiAssayExperiment",
ExperimentList = ExperimentList(list(foo = se)),
sampleMap = DataFrame(
assay = factor(character(), levels = "foo"),
primary = character(),
colname = character()
)
)
)
se0 <- matrix(runif(2), 1, 2, dimnames = list(letters[1], LETTERS[1:2]))
cd <- DataFrame(score = 1, row.names = paste0("pat", LETTERS[1]))
asamp <- DataFrame(assay = factor("bar"), primary = "patA", colname = "B")
## 1.iii. For each ExperimentList element, colnames must be found in the
## "assay" column of the sampleMap
expect_error(
new(
"MultiAssayExperiment",
ExperimentList = ExperimentList(list(bar = se0)),
colData = cd,
sampleMap = asamp
)
)
se <- matrix(runif(2), 1, 2, dimnames = list(letters[1], c("A", "A")))
cd <- DataFrame(score = 1, row.names = "patA")
asamp <- DataFrame(
assay = factor("foo"), primary = "patA", colname = "A"
)
## No duplicate colname identifiers within one assay
expect_error(
new(
"MultiAssayExperiment",
ExperimentList = ExperimentList(list(foo = se)),
colData = cd,
sampleMap = asamp
)
)
se <- matrix(runif(2), 1, 2, dimnames = list(letters[1], LETTERS[1:2]))
cd <- DataFrame(score = 1, row.names = "patA")
asamp <- DataFrame(assay = "foo", primary = "patA", colname = LETTERS[1:2])
## sampleMap assay column not a factor
expect_error(
new(
"MultiAssayExperiment",
ExperimentList = ExperimentList(list(foo = se)),
colData = cd,
sampleMap = asamp
)
)
})