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# This tests the pseudoBulkSpecific functions.
# library(testthat); library(scran); source("test-pseudo-spec.R")
set.seed(10000)
library(scuttle)
sce <- mockSCE(ncells=1000)
sce$samples <- gl(8, 125) # Pretending we have 8 samples.
# Making up some clusters.
sce <- logNormCounts(sce)
clusters <- kmeans(t(logcounts(sce)), centers=3)$cluster
# Creating a set of pseudo-bulk profiles:
info <- DataFrame(sample=sce$samples, cluster=clusters)
pseudo <- sumCountsAcrossCells(sce, info)
pseudo$DRUG <- gl(2,4)[pseudo$sample]
test_that("pseudoBulkSpecific works correctly in vanilla cases", {
# Spiking in DE for all clusters.
pseudo2 <- pseudo
xDRUG <- pseudo$DRUG
assay(pseudo2)[1,xDRUG==1] <- assay(pseudo2)[1,xDRUG==1] * 100
assay(pseudo2)[2,xDRUG==2] <- assay(pseudo2)[2,xDRUG==2] * 100
ref <- pseudoBulkDGE(pseudo2,
label=pseudo2$cluster,
design=~DRUG,
coef="DRUG2"
)
out <- pseudoBulkSpecific(pseudo2,
label=pseudo2$cluster,
design=~DRUG,
coef="DRUG2"
)
expect_identical(names(ref), names(out))
for (i in names(ref)) {
left <- ref[[i]]
right <- out[[i]]
expect_true(all(left$PValue <= right$PValue))
expect_identical(left$LogFC, right$LogFC)
expect_true(all(right$PValue[1:2] > 0.01))
expect_true(all(left$PValue[1:2] < 0.01))
}
# Also works for voom.
ref <- pseudoBulkDGE(pseudo2,
label=pseudo2$cluster,
design=~DRUG,
coef="DRUG2",
method="voom"
)
out <- pseudoBulkSpecific(pseudo2,
label=pseudo2$cluster,
design=~DRUG,
coef="DRUG2",
method="voom"
)
expect_identical(names(ref), names(out))
for (i in names(ref)) {
left <- ref[[i]]
right <- out[[i]]
expect_true(all(left$P.Value <= right$P.Value))
expect_identical(left$LogFC, right$LogFC)
expect_true(all(right$P.Value[1:2] > 0.05))
expect_true(all(left$P.Value[1:2] < 0.05))
}
})
test_that("pseudoBulkSpecific gives the same answers with a reference", {
out <- pseudoBulkSpecific(pseudo,
label=pseudo$cluster,
design=~DRUG,
coef="DRUG2"
)
ref <- pseudoBulkDGE(pseudo,
label=pseudo$cluster,
design=~DRUG,
coef="DRUG2"
)
metadata(ref)$tag <- "I'm here!"
metadata(ref[[1]])$tag <- "I'm still here!"
out2 <- pseudoBulkSpecific(pseudo,
label=pseudo$cluster,
design=~DRUG,
coef="DRUG2",
reference=ref
)
expect_identical(metadata(out2)$tag, "I'm here!")
expect_identical(metadata(out2[[1]])$tag, "I'm still here!")
metadata(out2)$tag <- NULL
metadata(out2[[1]])$tag <- NULL
expect_identical(out, out2)
})
test_that("pseudoBulkSpecific works correctly with sorting", {
ref <- pseudoBulkDGE(pseudo,
label=pseudo$cluster,
design=~DRUG,
coef="DRUG2"
)
out <- pseudoBulkSpecific(pseudo,
label=pseudo$cluster,
design=~DRUG,
coef="DRUG2",
reference=ref
)
out2 <- pseudoBulkSpecific(pseudo,
label=pseudo$cluster,
design=~DRUG,
coef="DRUG2",
reference=ref,
sorted=TRUE
)
for (i in names(ref)) {
left <- out[[i]]
right <- out2[[i]]
expect_identical(left[order(left$PValue),], right)
}
})
test_that("pseudoBulkSpecific works correctly with zero replacement", {
pseudo2 <- pseudo
assay(pseudo2)[1,pseudo2$cluster!=1] <- 0
ref <- pseudoBulkDGE(pseudo2,
label=pseudo2$cluster,
design=~DRUG,
coef="DRUG2"
)
out <- pseudoBulkSpecific(pseudo2,
label=pseudo2$cluster,
design=~DRUG,
coef="DRUG2",
reference=ref,
)
out2 <- pseudoBulkSpecific(pseudo2,
label=pseudo2$cluster,
design=~DRUG,
coef="DRUG2",
reference=ref,
missing.as.zero=TRUE
)
expect_identical(out[[1]]$OtherAverage[1], NA_real_)
expect_identical(out2[[1]]$OtherAverage[1], 0)
})
test_that("pseudoBulkSpecific errors out correctly", {
expect_error(pseudoBulkSpecific(pseudo,
label=pseudo$cluster,
design=~DRUG,
coef=1:2
), "cannot be specified")
})
|
