tests/testthat/test-ExperimentSubset.R
In campbio/ExperimentSubset: Manages subsets of data with Bioconductor Experiment objects
library(testthat)
library(SingleCellExperiment)
library(SummarizedExperiment)
library(ExperimentSubset)
library(scds)
library(TENxPBMCData)
library(scater)
library(scran)
library(airway)
#load data once
data(sce_chcl, package = "scds")
tenx_pbmc4k <- TENxPBMCData(dataset = "pbmc4k")
context("Testing ExperimentSubset functions")
testthat::test_that("Testing ExperimentSubset constructor by implicitly providing a SingleCellExperiment object",{
es <- ExperimentSubset(sce_chcl)
testthat::expect_true(validObject(es))
testthat::expect_equal(class(es)[1], "SubsetSingleCellExperiment")
})
testthat::test_that("Testing ExperimentSubset constructor by implicitly providing a SummarizedExperiment object",{
se <- SummarizedExperiment::SummarizedExperiment(sce_chcl)
testthat::expect_error(es <- ExperimentSubset(se), "Experiment objects with unnamed assays are not supported. Use assayNames<- setter method to set assay names before creating ES object.")
se <- SummarizedExperiment::SummarizedExperiment(list(counts = assay(sce_chcl, "counts"), logcounts = assay(sce_chcl, "logcounts")))
testthat::expect_s4_class(es <- ExperimentSubset(se), "SubsetSummarizedExperiment")
testthat::expect_true(validObject(es))
testthat::expect_equal(length(metadata(es)), 0)
testthat::expect_s4_class(assay(es, "counts"), "dgCMatrix")
es <- createSubset(es, "s1", rows = c(1:10))
testthat::expect_true("s1" %in% subsetNames(es))
testthat::expect_true("s1" %in% subsetAssayNames(es))
show(es)
es <- setSubsetAssay(es, "s1", assay(es, "s1"), "newS1")
testthat::expect_true("newS1" %in% subsetAssayNames(es))
testthat::expect_false("newS1" %in% subsetNames(es))
assay(es, "assay2") <- assay(es, "counts")
testthat::expect_true("assay2" %in% assayNames(es))
testthat::expect_equal(length(subsetParent(es, "s1")), 1)
subsetSummary(es)
testthat::expect_equal(subsetDim(es, "s1")[1], 10)
testthat::expect_equal(subsetDim(es, "s1")[2], 2000)
testthat::expect_equal(subsetCount(es), 1)
metadata(es) <- list(a="meta")
testthat::expect_equal(length(metadata(es)), 1)
testthat::expect_s4_class(getSubsetAssay(es, "s1"), "dgCMatrix")
subsetRownames(es, "s1") <- subsetRownames(es, "s1")
testthat::expect_equal(length(subsetRownames(es, "s1")), 10)
subsetColnames(es, "s1") <- subsetColnames(es, "s1")
testthat::expect_equal(length(subsetColnames(es, "s1")), 2000)
subsetRownames(es, "newS1") <- subsetRownames(es, "newS1")
testthat::expect_equal(length(subsetRownames(es, "newS1")), 10)
subsetColnames(es, "newS1") <- subsetColnames(es, "newS1")
testthat::expect_equal(length(subsetColnames(es, "newS1")), 2000)
colData(es, subsetName = "s1") <- cbind(colData(es, subsetName = "s1"),
DataFrame(col1 = c(seq(subsetDim(es, subsetName = "s1")[2]))))
testthat::expect_equal(ncol(colData(es, subsetName = "s1")), 1)
rowData(es, subsetName = "s1") <- cbind(rowData(es, subsetName = "s1"),
DataFrame(col1 = c(seq(subsetDim(es, subsetName = "s1")[1]))))
testthat::expect_equal(ncol(rowData(es, subsetName = "s1")), 1)
data(airway, package="airway")
rse <- airway
testthat::expect_s4_class(es <- ExperimentSubset(rse), "SubsetRangedSummarizedExperiment")
subsetSummary(es)
testthat::expect_equal(length(metadata(es)), 1)
es <- createSubset(es, "s2", rows = c(1:15))
testthat::expect_true("s2" %in% subsetNames(es))
testthat::expect_true("s2" %in% subsetAssayNames(es))
show(es)
es <- setSubsetAssay(es, "s2", assay(es, "s2"), "newS2")
testthat::expect_true("newS2" %in% subsetAssayNames(es))
testthat::expect_false("newS2" %in% subsetNames(es))
assay(es, "assay2") <- assay(es, "counts")
testthat::expect_true("assay2" %in% assayNames(es))
testthat::expect_equal(length(subsetParent(es, "s2")), 1)
subsetSummary(es)
testthat::expect_equal(subsetDim(es, "s2")[1], 15)
testthat::expect_equal(subsetDim(es, "s2")[2], 8)
testthat::expect_equal(subsetCount(es), 1)
metadata(es) <- list(a="meta")
testthat::expect_equal(length(metadata(es)), 1)
subsetRownames(es, "s2") <- subsetRownames(es, "s2")
testthat::expect_equal(length(subsetRownames(es, "s2")), 15)
subsetColnames(es, "s2") <- subsetColnames(es, "s2")
testthat::expect_equal(length(subsetColnames(es, "s2")), 8)
subsetRownames(es, "newS2") <- subsetRownames(es, "newS2")
testthat::expect_equal(length(subsetRownames(es, "newS2")), 15)
subsetColnames(es, "newS2") <- subsetColnames(es, "newS2")
testthat::expect_equal(length(subsetColnames(es, "newS2")), 8)
colData(es, subsetName = "s2") <- cbind(colData(es, subsetName = "s2"),
DataFrame(col1 = c(seq(subsetDim(es, subsetName = "s2")[2]))))
testthat::expect_equal(ncol(colData(es, subsetName = "s2", parentColData = TRUE)), 10)
rowData(es, subsetName = "s2") <- cbind(rowData(es, subsetName = "s2"),
DataFrame(col1 = c(seq(subsetDim(es, subsetName = "s2")[1]))))
testthat::expect_equal(ncol(rowData(es, subsetName = "s2")), 1)
testthat::expect_error(es <- createSubset(es, "s2", rows = c(1:15)),
"A subset with the specified 'subsetName' parameter already exists
in the object. Subset names must be unique.")
testthat::expect_error(es <- createSubset(es, subsetName = 12, rows = c(1:15)),
"'subsetName' parameter must be a unique a character value.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", rows = list()),
"'rows' parameter must be either a 'NULL' to include all rows,
or a numeric vector or a character vector that specify the rows to
include in the subset.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", cols = list()),
"'cols' parameter must be either a 'NULL' to include all rows,
or a numeric vector or a character vector that specify the columns to
include in the subset.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", parentAssay = 1),
"'parentAssay' parameter can either be 'NULL' to use the default
assay in the input object or a character value that specifies the
parentAssay to use from parent object.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", rows = c(64103:64103)),
"Selected rows not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", rows = c(seq(1:64102), 64102)),
"Selected rows not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", rows = c(1,3, NA)),
"Selected rows not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", cols = c(10:12)),
"Selected columns not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", cols = c(seq(1:8), 8)),
"Selected columns not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", cols = c(1,3, NA)),
"Selected columns not available in the specified assay.")
})
testthat::test_that("Testing ExperimentSubset constructor with subset & createSubset without parentAssay",{
es <- ExperimentSubset(sce_chcl, subset = list(subsetName = "subset10", rows = c(1:10), cols = c(1:2), parentAssay = "counts"))
testthat::expect_equal(es@subsets$subset1@subsetName, "subset10")
testthat::expect_equal(es@subsets$subset1@rowIndices, c(1:10))
testthat::expect_equal(es@subsets$subset1@colIndices, c(1:2))
testthat::expect_equal(es@subsets$subset1@parentAssay, "counts")
es <- createSubset(es, "subset1", rows = c(10,11,50,56,98,99,102,105,109, 200), cols = c(20,21,40,45,90,99,100,123,166,299))
testthat::expect_equal(es@subsets$subset1@subsetName, "subset1")
testthat::expect_equal(es@subsets$subset1@rowIndices, c(10,11,50,56,98,99,102,105,109, 200))
testthat::expect_equal(es@subsets$subset1@colIndices, c(20,21,40,45,90,99,100,123,166,299))
testthat::expect_equal(es@subsets$subset1@parentAssay, "counts")
})
testthat::test_that("Testing createSubset and setSubsetAssay",{
es <- ExperimentSubset(sce_chcl)
#createSubset
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109,200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
testthat::expect_equal(es@subsets$subset1@subsetName, "subset1")
testthat::expect_equal(es@subsets$subset1@rowIndices, c(10,11,50,56,98,99,102,105,109,200))
testthat::expect_equal(es@subsets$subset1@colIndices, c(20,21,40,45,90,99,100,123,166,299))
testthat::expect_equal(es@subsets$subset1@parentAssay, "counts")
subsetRownames(es, "subset1") <- subsetRownames(es, "subset1")
subsetColnames(es, "subset1") <- subsetColnames(es, "subset1")
subsetRownames(es, "subset1") <- subsetRownames(es, "subset1")
subsetColnames(es, "subset1") <- subsetColnames(es, "subset1")
es <- createSubset(es, "subset2",
rows = c("OPCML", "RP11-338K17.8", "RP11-770J1.3", "NPSR1", "AC060835.1", "GABRA2", "PRDM16", "CAB39", "LYRM1", "RP1-178F10.3"),
cols = c("TTAGTTCTCGTAGGAG", "GGCTGGTGTCTCGTTC", "TCGCGTTGTTAAGTAG", "GGATGTTGTAGGCATG", "AATCGGTTCTGATACG", "GTTCTCGGTATGAAAC", "TCCACACTCTTTAGTC", "GCGCAGTAGATGCGAC", "CGGACACTCAAGAAGT", "TGACTTTGTCGCGAAA"),
parentAssay = "counts")
testthat::expect_equal(es@subsets$subset2@subsetName, "subset2")
testthat::expect_equal(es@subsets$subset2@rowIndices, c(10,11,50,56,98,99,102,105,109,200))
testthat::expect_equal(es@subsets$subset2@colIndices, c(20,21,40,45,90,99,100,123,166,299))
testthat::expect_equal(es@subsets$subset2@parentAssay, "counts")
# expect_error(es <- createSubset(es, "subset3",
# rows = c("OPCML", "RP11-338K17.8", 50,56,98,99,102,105,109,200),
# cols = c("TTAGTTCTCGTAGGAG", "GGCTGGTGTCTCGTTC", "TCGCGTTGTTAAGTAG", "GGATGTTGTAGGCATG", "AATCGGTTCTGATACG", "GTTCTCGGTATGAAAC", "TCCACACTCTTTAGTC", "GCGCAGTAGATGCGAC", "CGGACACTCAAGAAGT", "TGACTTTGTCGCGAAA"),
# parentAssay = "counts"), "NAs introduced in input rows or columns. Some or all indicated rows or columns not found in specified parent.")
#setSubsetAssay
counts1p <- assay(es, "subset1")
counts1p[,] <- counts1p[,] + 1
expect_error(es <- setSubsetAssay(es, "subset4", counts1p, "scaledSubset1"),
"subset4 does not exist in the subsets slot of the object.")
es <- setSubsetAssay(es, "subset1", counts1p, "scaledSubset1")
expect_true("scaledSubset1" %in% assayNames(es@subsets$subset1@internalAssay))
getSubsetAssay(es, "scaledSubset1")
# expect_error(es <- setSubsetAssay(es, "subset1", counts1p, subsetAssayName = NULL),
# "subset1 already exists. Please choose a different subsetName parameter.")
# es <- setSubsetAssay(es, "subset4", counts1p, subsetAssayName = NULL)
# expect_equal(rownames(counts1p), rownames(es, "subset4"))
# expect_equal(colnames(counts1p), colnames(es, "subset4"))
#cant have null now
})
testthat::test_that("Testing rownames, colnames, rowData and colData",{
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109,200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
counts1p <- assay(es, "subset1")
counts1p[,] <- counts1p[,] + 1
es <- setSubsetAssay(es, "subset1", counts1p, "scaledSubset1")
# expect_equal(rownames(es, subsetName = "scaledSubset1"), rownames(counts1p))
# expect_equal(colnames(es, subsetName = "scaledSubset1"), colnames(counts1p))
# expect_equal(rownames(es, subsetName = "subset1"), rownames(es)[c(10,11,50,56,98,99,102,105,109,200)])
# expect_equal(colnames(es, subsetName = "subset1"), colnames(es)[c(20,21,40,45,90,99,100,123,166,299)])
testthat::expect_error(colData(es, subsetName = "subset1Internal"),
"subset1Internal subset does not exist.")
testthat::expect_error(rowData(es, subsetName = "subset1Internal"),
"subset1Internal subset does not exist.")
rowData(es, subsetName = "subset1") <- DataFrame(col1 = c(seq(subsetDim(es, subsetName = "subset1")[1])))
colData(es, subsetName = "subset1") <- DataFrame(col1 = c(seq(subsetDim(es, subsetName = "subset1")[2])))
expect_equal(ncol(rowData(es, subsetName = "subset1", parentRowData = TRUE)), 2)
expect_equal(nrow(rowData(es, subsetName = "subset1", parentRowData = TRUE)), subsetDim(es, subsetName = "subset1")[1])
expect_equal(ncol(colData(es, subsetName = "subset1", parentColData = TRUE)), 12)
expect_equal(nrow(rowData(es, subsetName = "subset1", parentColData = TRUE)), subsetDim(es, subsetName = "subset1")[2])
})
testthat::test_that("Testing subset helper/supplementary functions",{
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109,200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
counts1p <- assay(es, "subset1")
counts1p[,] <- counts1p[,] + 1
es <- setSubsetAssay(es, "subset1", counts1p, "scaledSubset1")
expect_equal(subsetCount(es), 1)
expect_equal(subsetAssayCount(es), 2)
expect_equal(subsetAssayNames(es), c("subset1", "scaledSubset1"))
expect_equal(subsetNames(es), "subset1")
subsetSummary(es)
expect_equal(subsetParent(es, "scaledSubset1"), list("subset1", "counts"))
show(es)
})
testthat::test_that("Testing assay function",{
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109,200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
es@subsets$subset1@parentAssay <- "counts"
subset1Assay <- assay(es, "subset1")
expect_true(all.equal(subset1Assay, assay(es, "counts")[c(10,11,50,56,98,99,102,105,109,200), c(20,21,40,45,90,99,100,123,166,299)]))
assay(es, "counts2") <- assay(es, "counts")
expect_true(all.equal(assay(es, "counts"), assay(es, "counts2")))
})
#create es with pbmc4k data, compute colsums and rowsums, create a hvg1000 subset for further testing
es <- ExperimentSubset(tenx_pbmc4k)
colData(es) <- cbind(colData(es), colSums = colSums(assay(es, "counts")))
rowData(es) <- cbind(rowData(es), rowSums = rowSums(assay(es, "counts")))
es <- createSubset(es, "filteredAssay", rows = rownames(es), cols = which(colData(es)$colSums > mean(colData(es)$colSums)), parentAssay = "counts")
assay(es, "filteredAssay", withDimnames = FALSE, subsetAssayName = "filteredAssayNormalized") <- scater::normalizeCounts(assay(es, "filteredAssay"))
es <- createSubset(es, "hvg1000", rows = scran::getTopHVGs(scran::modelGeneVar(assay(es, "filteredAssayNormalized")), n = 1000), cols = seq(1:1622), parentAssay = "filteredAssayNormalized")
testthat::test_that("Testing reducedDims",{
set.seed(20)
colData(es, subsetName = "hvg1000") <- cbind(colData(es, subsetName = "hvg1000"), cluster = kmeans(t(assay(es, "hvg1000")), 5)$cluster)
expect_true("cluster" %in% colnames(colData(es, subsetName = "hvg1000")))
reducedDim(es, type = "PCA", subsetName = "hvg1000") <- scater::calculatePCA(assay(es, "hvg1000"))
expect_true("PCA" %in% reducedDimNames(es, subsetName = "hvg1000"))
reducedDims(es, subsetName = "hvg1000") <- list(a = scater::calculatePCA(assay(es, "hvg1000")), b = scater::calculatePCA(assay(es, "hvg1000")))
expect_true(all.equal(reducedDimNames(es, subsetName = "hvg1000"), c("a","b")))
reducedDimNames(es, subsetName = "hvg1000") <- c("PCA_1", "PCA_2")
expect_true(all.equal(reducedDimNames(es, subsetName = "hvg1000"), c("PCA_1", "PCA_2")))
testthat::expect_error(reducedDimNames(es, subsetName = "hvg123"),
"hvg123 subset does not exist.")
testthat::expect_error(reducedDimNames(es, subsetName = "hvg123") <- c("PCA_1"),
"hvg123 does not exist in the subsets slot of the object.")
reducedDim(es, type = "PCA") <- scater::calculatePCA(assay(es, "counts"))
expect_true(!is.null(reducedDim(es, type = "PCA")))
reducedDims(es) <- list(a = scater::calculatePCA(assay(es, "counts")), b = scater::calculatePCA(assay(es, "counts")))
expect_true(!is.null(reducedDims(es)))
expect_true(all.equal(reducedDimNames(es), c("a", "b")))
reducedDimNames(es) <- c("PCA_Counts_1", "PCA_Counts_2")
expect_true(all.equal(reducedDimNames(es), c("PCA_Counts_1", "PCA_Counts_2")))
})
testthat::test_that("Testing metadata",{
metadata(es, subsetName = "hvg1000") <- list(meta1 = "This is testing meta1", meta2 = "This is testing meta2")
expect_equal(metadata(es, subsetName = "hvg1000")$meta1, "This is testing meta1")
expect_equal(metadata(es, subsetName = "hvg1000")$meta2, "This is testing meta2")
testthat::expect_error(metadata(es, subsetName = "hvg") <- list(meta1 = "This is testing meta1", meta2 = "This is testing meta2"),
"hvg subset does not exist.")
testthat::expect_error(metadata(es, subsetName = "hvg"),
"hvg subset does not exist.")
metadata(es) <- list(meta1 = "This is testing meta1", meta2 = "This is testing meta2")
expect_equal(metadata(es)$meta1, "This is testing meta1")
expect_equal(metadata(es)$meta2, "This is testing meta2")
})
testthat::test_that("Testing altExperiments",{
altExp(es, "alt1", subsetName = "hvg1000") <- es@subsets$hvg1000@internalAssay
altExp(es, "alt2", subsetName = "hvg1000") <- es@subsets$hvg1000@internalAssay
expect_true(all.equal(altExpNames(es, subsetName = "hvg1000"), c("alt1", "alt2")))
testthat::expect_error(altExp(es, "alt1", subsetName = "hvg") <- es@subsets$hvg1000@internalAssay,
"hvg subset does not exist.")
altExp(es, subsetName = "hvg1000") <- es@subsets$hvg1000@internalAssay
expect_equal(length(altExpNames(es, subsetName = "hvg1000")), 2)
expect_true(!is.null(altExp(es, subsetName = "hvg1000")))
altExp(es) <- tenx_pbmc4k
expect_true(!is.null(altExp(es)))
altExp(es, "a1") <- tenx_pbmc4k
expect_true("a1" %in% altExpNames(es))
expect_true(!is.null(altExp(es, "a1")))
testthat::expect_error(altExpNames(es, subsetName = "na"),
"na subset does not exist.")
testthat::expect_error(altExpNames(es, subsetName = "na") <- c("na2"),
"na subset does not exist.")
altExpNames(es) <- c("a1", "a2")
expect_true(all.equal(altExpNames(es), c("a1", "a2")))
testthat::expect_error(altExp(es, "alt1", subsetName = "hvg10002"),
"hvg10002 subset does not exist.")
altExpNames(es, subsetName = "hvg1000") <- c("a1", "a2")
expect_true(all.equal(altExpNames(es, subsetName = "hvg1000"), c("a1", "a2")))
testthat::expect_error(altExpNames(es, subsetName = "hvg1000x"),
"hvg1000x subset does not exist.")
altExps(es, subsetName = "hvg1000") <- list(a = es@subsets$hvg1000@internalAssay, b = es@subsets$hvg1000@internalAssay)
expect_true(all.equal(altExpNames(es, subsetName = "hvg1000"), c("a","b")))
testthat::expect_error(altExps(es, subsetName = "hvg") <- list(a = es@subsets$hvg1000@internalAssay, b = es@subsets$hvg1000@internalAssay),
"hvg subset does not exist.")
testthat::expect_error(altExps(es, subsetName = "hvg10002"),
"hvg10002 subset does not exist.")
altExps(es) <- list(a = tenx_pbmc4k, b = tenx_pbmc4k)
expect_true(all.equal(altExpNames(es), c("a", "b")))
}
)
testthat::test_that("Testing createSubset with multiple paramter options",{
es <- ExperimentSubset(sce_chcl)
testthat::expect_error(es <- createSubset(es, "subset1", rows = c(10,11,50,56,98,99,102,105,109, 200), cols = c(20,21,40,45,90,99,100,123,166,299), parentAssay = "none"), "Input parentAssay does not exist.")
#colnames
es <- createSubset(es, "subset1", rows = c(10,11,50,56,98,99,102,105,109, 200), cols = c("CTGCTGTCAGGGTATG", "CAGTCCTTCGGTTAAC"), parentAssay = "counts")
testthat::expect_equal(es@subsets$subset1@subsetName, "subset1")
testthat::expect_equal(es@subsets$subset1@rowIndices, c(10,11,50,56,98,99,102,105,109, 200))
testthat::expect_equal(es@subsets$subset1@colIndices, match(c("CTGCTGTCAGGGTATG", "CAGTCCTTCGGTTAAC"), subsetColnames(es, subsetName = "subset1")))
testthat::expect_equal(es@subsets$subset1@parentAssay, "counts")
#null rows and null cols
es <- createSubset(es, "subset2", parentAssay = "counts")
testthat::expect_equal(es@subsets$subset2@subsetName, "subset2")
testthat::expect_equal(es@subsets$subset2@rowIndices, c(1:subsetDim(es, "subset2")[1]))
testthat::expect_equal(es@subsets$subset2@colIndices, c(1:subsetDim(es, "subset2")[2]))
testthat::expect_equal(es@subsets$subset2@parentAssay, "counts")
#nas introduced in rows or cols : update: this error is changed and does not appear in this way
# testthat::expect_error(es <- createSubset(es, "subset22", rows = c("as", "asd", "asd"), cols = c("CTGCTGTCAGGGTATG", "CAGTCCTTCGGTTAAC"), parentAssay = "counts"), "NAs introduced in input rows or columns. Some or all indicated rows or columns not found in specified parent.")
# testthat::expect_error(es <- createSubset(es, "subset22", cols = c("CTGTG", "CAGTCC"), parentAssay = "counts"), "NAs introduced in input rows or columns. Some or all indicated rows or columns not found in specified parent.")
})
testthat::test_that("Completing test coverage, move this into relevant places later",{
es <- ExperimentSubset(sce_chcl)
testthat::expect_warning(es <- createSubset(es, "subset 1", rows = c(1:5), cols = (1:5)),
"Removing spaces from the specified subsetName.")
es <- ExperimentSubset(list(counts = assay(sce_chcl, "counts")))
})
campbio/ExperimentSubset documentation built on Sept. 10, 2021, 3:09 p.m.
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library(testthat)
library(SingleCellExperiment)
library(SummarizedExperiment)
library(ExperimentSubset)
library(scds)
library(TENxPBMCData)
library(scater)
library(scran)
library(airway)
#load data once
data(sce_chcl, package = "scds")
tenx_pbmc4k <- TENxPBMCData(dataset = "pbmc4k")
context("Testing ExperimentSubset functions")
testthat::test_that("Testing ExperimentSubset constructor by implicitly providing a SingleCellExperiment object",{
es <- ExperimentSubset(sce_chcl)
testthat::expect_true(validObject(es))
testthat::expect_equal(class(es)[1], "SubsetSingleCellExperiment")
})
testthat::test_that("Testing ExperimentSubset constructor by implicitly providing a SummarizedExperiment object",{
se <- SummarizedExperiment::SummarizedExperiment(sce_chcl)
testthat::expect_error(es <- ExperimentSubset(se), "Experiment objects with unnamed assays are not supported. Use assayNames<- setter method to set assay names before creating ES object.")
se <- SummarizedExperiment::SummarizedExperiment(list(counts = assay(sce_chcl, "counts"), logcounts = assay(sce_chcl, "logcounts")))
testthat::expect_s4_class(es <- ExperimentSubset(se), "SubsetSummarizedExperiment")
testthat::expect_true(validObject(es))
testthat::expect_equal(length(metadata(es)), 0)
testthat::expect_s4_class(assay(es, "counts"), "dgCMatrix")
es <- createSubset(es, "s1", rows = c(1:10))
testthat::expect_true("s1" %in% subsetNames(es))
testthat::expect_true("s1" %in% subsetAssayNames(es))
show(es)
es <- setSubsetAssay(es, "s1", assay(es, "s1"), "newS1")
testthat::expect_true("newS1" %in% subsetAssayNames(es))
testthat::expect_false("newS1" %in% subsetNames(es))
assay(es, "assay2") <- assay(es, "counts")
testthat::expect_true("assay2" %in% assayNames(es))
testthat::expect_equal(length(subsetParent(es, "s1")), 1)
subsetSummary(es)
testthat::expect_equal(subsetDim(es, "s1")[1], 10)
testthat::expect_equal(subsetDim(es, "s1")[2], 2000)
testthat::expect_equal(subsetCount(es), 1)
metadata(es) <- list(a="meta")
testthat::expect_equal(length(metadata(es)), 1)
testthat::expect_s4_class(getSubsetAssay(es, "s1"), "dgCMatrix")
subsetRownames(es, "s1") <- subsetRownames(es, "s1")
testthat::expect_equal(length(subsetRownames(es, "s1")), 10)
subsetColnames(es, "s1") <- subsetColnames(es, "s1")
testthat::expect_equal(length(subsetColnames(es, "s1")), 2000)
subsetRownames(es, "newS1") <- subsetRownames(es, "newS1")
testthat::expect_equal(length(subsetRownames(es, "newS1")), 10)
subsetColnames(es, "newS1") <- subsetColnames(es, "newS1")
testthat::expect_equal(length(subsetColnames(es, "newS1")), 2000)
colData(es, subsetName = "s1") <- cbind(colData(es, subsetName = "s1"),
DataFrame(col1 = c(seq(subsetDim(es, subsetName = "s1")[2]))))
testthat::expect_equal(ncol(colData(es, subsetName = "s1")), 1)
rowData(es, subsetName = "s1") <- cbind(rowData(es, subsetName = "s1"),
DataFrame(col1 = c(seq(subsetDim(es, subsetName = "s1")[1]))))
testthat::expect_equal(ncol(rowData(es, subsetName = "s1")), 1)
data(airway, package="airway")
rse <- airway
testthat::expect_s4_class(es <- ExperimentSubset(rse), "SubsetRangedSummarizedExperiment")
subsetSummary(es)
testthat::expect_equal(length(metadata(es)), 1)
es <- createSubset(es, "s2", rows = c(1:15))
testthat::expect_true("s2" %in% subsetNames(es))
testthat::expect_true("s2" %in% subsetAssayNames(es))
show(es)
es <- setSubsetAssay(es, "s2", assay(es, "s2"), "newS2")
testthat::expect_true("newS2" %in% subsetAssayNames(es))
testthat::expect_false("newS2" %in% subsetNames(es))
assay(es, "assay2") <- assay(es, "counts")
testthat::expect_true("assay2" %in% assayNames(es))
testthat::expect_equal(length(subsetParent(es, "s2")), 1)
subsetSummary(es)
testthat::expect_equal(subsetDim(es, "s2")[1], 15)
testthat::expect_equal(subsetDim(es, "s2")[2], 8)
testthat::expect_equal(subsetCount(es), 1)
metadata(es) <- list(a="meta")
testthat::expect_equal(length(metadata(es)), 1)
subsetRownames(es, "s2") <- subsetRownames(es, "s2")
testthat::expect_equal(length(subsetRownames(es, "s2")), 15)
subsetColnames(es, "s2") <- subsetColnames(es, "s2")
testthat::expect_equal(length(subsetColnames(es, "s2")), 8)
subsetRownames(es, "newS2") <- subsetRownames(es, "newS2")
testthat::expect_equal(length(subsetRownames(es, "newS2")), 15)
subsetColnames(es, "newS2") <- subsetColnames(es, "newS2")
testthat::expect_equal(length(subsetColnames(es, "newS2")), 8)
colData(es, subsetName = "s2") <- cbind(colData(es, subsetName = "s2"),
DataFrame(col1 = c(seq(subsetDim(es, subsetName = "s2")[2]))))
testthat::expect_equal(ncol(colData(es, subsetName = "s2", parentColData = TRUE)), 10)
rowData(es, subsetName = "s2") <- cbind(rowData(es, subsetName = "s2"),
DataFrame(col1 = c(seq(subsetDim(es, subsetName = "s2")[1]))))
testthat::expect_equal(ncol(rowData(es, subsetName = "s2")), 1)
testthat::expect_error(es <- createSubset(es, "s2", rows = c(1:15)),
"A subset with the specified 'subsetName' parameter already exists
in the object. Subset names must be unique.")
testthat::expect_error(es <- createSubset(es, subsetName = 12, rows = c(1:15)),
"'subsetName' parameter must be a unique a character value.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", rows = list()),
"'rows' parameter must be either a 'NULL' to include all rows,
or a numeric vector or a character vector that specify the rows to
include in the subset.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", cols = list()),
"'cols' parameter must be either a 'NULL' to include all rows,
or a numeric vector or a character vector that specify the columns to
include in the subset.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", parentAssay = 1),
"'parentAssay' parameter can either be 'NULL' to use the default
assay in the input object or a character value that specifies the
parentAssay to use from parent object.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", rows = c(64103:64103)),
"Selected rows not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", rows = c(seq(1:64102), 64102)),
"Selected rows not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", rows = c(1,3, NA)),
"Selected rows not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", cols = c(10:12)),
"Selected columns not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", cols = c(seq(1:8), 8)),
"Selected columns not available in the specified assay.")
testthat::expect_error(es <- createSubset(es, subsetName = "s3", cols = c(1,3, NA)),
"Selected columns not available in the specified assay.")
})
testthat::test_that("Testing ExperimentSubset constructor with subset & createSubset without parentAssay",{
es <- ExperimentSubset(sce_chcl, subset = list(subsetName = "subset10", rows = c(1:10), cols = c(1:2), parentAssay = "counts"))
testthat::expect_equal(es@subsets$subset1@subsetName, "subset10")
testthat::expect_equal(es@subsets$subset1@rowIndices, c(1:10))
testthat::expect_equal(es@subsets$subset1@colIndices, c(1:2))
testthat::expect_equal(es@subsets$subset1@parentAssay, "counts")
es <- createSubset(es, "subset1", rows = c(10,11,50,56,98,99,102,105,109, 200), cols = c(20,21,40,45,90,99,100,123,166,299))
testthat::expect_equal(es@subsets$subset1@subsetName, "subset1")
testthat::expect_equal(es@subsets$subset1@rowIndices, c(10,11,50,56,98,99,102,105,109, 200))
testthat::expect_equal(es@subsets$subset1@colIndices, c(20,21,40,45,90,99,100,123,166,299))
testthat::expect_equal(es@subsets$subset1@parentAssay, "counts")
})
testthat::test_that("Testing createSubset and setSubsetAssay",{
es <- ExperimentSubset(sce_chcl)
#createSubset
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109,200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
testthat::expect_equal(es@subsets$subset1@subsetName, "subset1")
testthat::expect_equal(es@subsets$subset1@rowIndices, c(10,11,50,56,98,99,102,105,109,200))
testthat::expect_equal(es@subsets$subset1@colIndices, c(20,21,40,45,90,99,100,123,166,299))
testthat::expect_equal(es@subsets$subset1@parentAssay, "counts")
subsetRownames(es, "subset1") <- subsetRownames(es, "subset1")
subsetColnames(es, "subset1") <- subsetColnames(es, "subset1")
subsetRownames(es, "subset1") <- subsetRownames(es, "subset1")
subsetColnames(es, "subset1") <- subsetColnames(es, "subset1")
es <- createSubset(es, "subset2",
rows = c("OPCML", "RP11-338K17.8", "RP11-770J1.3", "NPSR1", "AC060835.1", "GABRA2", "PRDM16", "CAB39", "LYRM1", "RP1-178F10.3"),
cols = c("TTAGTTCTCGTAGGAG", "GGCTGGTGTCTCGTTC", "TCGCGTTGTTAAGTAG", "GGATGTTGTAGGCATG", "AATCGGTTCTGATACG", "GTTCTCGGTATGAAAC", "TCCACACTCTTTAGTC", "GCGCAGTAGATGCGAC", "CGGACACTCAAGAAGT", "TGACTTTGTCGCGAAA"),
parentAssay = "counts")
testthat::expect_equal(es@subsets$subset2@subsetName, "subset2")
testthat::expect_equal(es@subsets$subset2@rowIndices, c(10,11,50,56,98,99,102,105,109,200))
testthat::expect_equal(es@subsets$subset2@colIndices, c(20,21,40,45,90,99,100,123,166,299))
testthat::expect_equal(es@subsets$subset2@parentAssay, "counts")
# expect_error(es <- createSubset(es, "subset3",
# rows = c("OPCML", "RP11-338K17.8", 50,56,98,99,102,105,109,200),
# cols = c("TTAGTTCTCGTAGGAG", "GGCTGGTGTCTCGTTC", "TCGCGTTGTTAAGTAG", "GGATGTTGTAGGCATG", "AATCGGTTCTGATACG", "GTTCTCGGTATGAAAC", "TCCACACTCTTTAGTC", "GCGCAGTAGATGCGAC", "CGGACACTCAAGAAGT", "TGACTTTGTCGCGAAA"),
# parentAssay = "counts"), "NAs introduced in input rows or columns. Some or all indicated rows or columns not found in specified parent.")
#setSubsetAssay
counts1p <- assay(es, "subset1")
counts1p[,] <- counts1p[,] + 1
expect_error(es <- setSubsetAssay(es, "subset4", counts1p, "scaledSubset1"),
"subset4 does not exist in the subsets slot of the object.")
es <- setSubsetAssay(es, "subset1", counts1p, "scaledSubset1")
expect_true("scaledSubset1" %in% assayNames(es@subsets$subset1@internalAssay))
getSubsetAssay(es, "scaledSubset1")
# expect_error(es <- setSubsetAssay(es, "subset1", counts1p, subsetAssayName = NULL),
# "subset1 already exists. Please choose a different subsetName parameter.")
# es <- setSubsetAssay(es, "subset4", counts1p, subsetAssayName = NULL)
# expect_equal(rownames(counts1p), rownames(es, "subset4"))
# expect_equal(colnames(counts1p), colnames(es, "subset4"))
#cant have null now
})
testthat::test_that("Testing rownames, colnames, rowData and colData",{
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109,200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
counts1p <- assay(es, "subset1")
counts1p[,] <- counts1p[,] + 1
es <- setSubsetAssay(es, "subset1", counts1p, "scaledSubset1")
# expect_equal(rownames(es, subsetName = "scaledSubset1"), rownames(counts1p))
# expect_equal(colnames(es, subsetName = "scaledSubset1"), colnames(counts1p))
# expect_equal(rownames(es, subsetName = "subset1"), rownames(es)[c(10,11,50,56,98,99,102,105,109,200)])
# expect_equal(colnames(es, subsetName = "subset1"), colnames(es)[c(20,21,40,45,90,99,100,123,166,299)])
testthat::expect_error(colData(es, subsetName = "subset1Internal"),
"subset1Internal subset does not exist.")
testthat::expect_error(rowData(es, subsetName = "subset1Internal"),
"subset1Internal subset does not exist.")
rowData(es, subsetName = "subset1") <- DataFrame(col1 = c(seq(subsetDim(es, subsetName = "subset1")[1])))
colData(es, subsetName = "subset1") <- DataFrame(col1 = c(seq(subsetDim(es, subsetName = "subset1")[2])))
expect_equal(ncol(rowData(es, subsetName = "subset1", parentRowData = TRUE)), 2)
expect_equal(nrow(rowData(es, subsetName = "subset1", parentRowData = TRUE)), subsetDim(es, subsetName = "subset1")[1])
expect_equal(ncol(colData(es, subsetName = "subset1", parentColData = TRUE)), 12)
expect_equal(nrow(rowData(es, subsetName = "subset1", parentColData = TRUE)), subsetDim(es, subsetName = "subset1")[2])
})
testthat::test_that("Testing subset helper/supplementary functions",{
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109,200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
counts1p <- assay(es, "subset1")
counts1p[,] <- counts1p[,] + 1
es <- setSubsetAssay(es, "subset1", counts1p, "scaledSubset1")
expect_equal(subsetCount(es), 1)
expect_equal(subsetAssayCount(es), 2)
expect_equal(subsetAssayNames(es), c("subset1", "scaledSubset1"))
expect_equal(subsetNames(es), "subset1")
subsetSummary(es)
expect_equal(subsetParent(es, "scaledSubset1"), list("subset1", "counts"))
show(es)
})
testthat::test_that("Testing assay function",{
es <- ExperimentSubset(sce_chcl)
es <- createSubset(es, "subset1",
rows = c(10,11,50,56,98,99,102,105,109,200),
cols = c(20,21,40,45,90,99,100,123,166,299),
parentAssay = "counts")
es@subsets$subset1@parentAssay <- "counts"
subset1Assay <- assay(es, "subset1")
expect_true(all.equal(subset1Assay, assay(es, "counts")[c(10,11,50,56,98,99,102,105,109,200), c(20,21,40,45,90,99,100,123,166,299)]))
assay(es, "counts2") <- assay(es, "counts")
expect_true(all.equal(assay(es, "counts"), assay(es, "counts2")))
})
#create es with pbmc4k data, compute colsums and rowsums, create a hvg1000 subset for further testing
es <- ExperimentSubset(tenx_pbmc4k)
colData(es) <- cbind(colData(es), colSums = colSums(assay(es, "counts")))
rowData(es) <- cbind(rowData(es), rowSums = rowSums(assay(es, "counts")))
es <- createSubset(es, "filteredAssay", rows = rownames(es), cols = which(colData(es)$colSums > mean(colData(es)$colSums)), parentAssay = "counts")
assay(es, "filteredAssay", withDimnames = FALSE, subsetAssayName = "filteredAssayNormalized") <- scater::normalizeCounts(assay(es, "filteredAssay"))
es <- createSubset(es, "hvg1000", rows = scran::getTopHVGs(scran::modelGeneVar(assay(es, "filteredAssayNormalized")), n = 1000), cols = seq(1:1622), parentAssay = "filteredAssayNormalized")
testthat::test_that("Testing reducedDims",{
set.seed(20)
colData(es, subsetName = "hvg1000") <- cbind(colData(es, subsetName = "hvg1000"), cluster = kmeans(t(assay(es, "hvg1000")), 5)$cluster)
expect_true("cluster" %in% colnames(colData(es, subsetName = "hvg1000")))
reducedDim(es, type = "PCA", subsetName = "hvg1000") <- scater::calculatePCA(assay(es, "hvg1000"))
expect_true("PCA" %in% reducedDimNames(es, subsetName = "hvg1000"))
reducedDims(es, subsetName = "hvg1000") <- list(a = scater::calculatePCA(assay(es, "hvg1000")), b = scater::calculatePCA(assay(es, "hvg1000")))
expect_true(all.equal(reducedDimNames(es, subsetName = "hvg1000"), c("a","b")))
reducedDimNames(es, subsetName = "hvg1000") <- c("PCA_1", "PCA_2")
expect_true(all.equal(reducedDimNames(es, subsetName = "hvg1000"), c("PCA_1", "PCA_2")))
testthat::expect_error(reducedDimNames(es, subsetName = "hvg123"),
"hvg123 subset does not exist.")
testthat::expect_error(reducedDimNames(es, subsetName = "hvg123") <- c("PCA_1"),
"hvg123 does not exist in the subsets slot of the object.")
reducedDim(es, type = "PCA") <- scater::calculatePCA(assay(es, "counts"))
expect_true(!is.null(reducedDim(es, type = "PCA")))
reducedDims(es) <- list(a = scater::calculatePCA(assay(es, "counts")), b = scater::calculatePCA(assay(es, "counts")))
expect_true(!is.null(reducedDims(es)))
expect_true(all.equal(reducedDimNames(es), c("a", "b")))
reducedDimNames(es) <- c("PCA_Counts_1", "PCA_Counts_2")
expect_true(all.equal(reducedDimNames(es), c("PCA_Counts_1", "PCA_Counts_2")))
})
testthat::test_that("Testing metadata",{
metadata(es, subsetName = "hvg1000") <- list(meta1 = "This is testing meta1", meta2 = "This is testing meta2")
expect_equal(metadata(es, subsetName = "hvg1000")$meta1, "This is testing meta1")
expect_equal(metadata(es, subsetName = "hvg1000")$meta2, "This is testing meta2")
testthat::expect_error(metadata(es, subsetName = "hvg") <- list(meta1 = "This is testing meta1", meta2 = "This is testing meta2"),
"hvg subset does not exist.")
testthat::expect_error(metadata(es, subsetName = "hvg"),
"hvg subset does not exist.")
metadata(es) <- list(meta1 = "This is testing meta1", meta2 = "This is testing meta2")
expect_equal(metadata(es)$meta1, "This is testing meta1")
expect_equal(metadata(es)$meta2, "This is testing meta2")
})
testthat::test_that("Testing altExperiments",{
altExp(es, "alt1", subsetName = "hvg1000") <- es@subsets$hvg1000@internalAssay
altExp(es, "alt2", subsetName = "hvg1000") <- es@subsets$hvg1000@internalAssay
expect_true(all.equal(altExpNames(es, subsetName = "hvg1000"), c("alt1", "alt2")))
testthat::expect_error(altExp(es, "alt1", subsetName = "hvg") <- es@subsets$hvg1000@internalAssay,
"hvg subset does not exist.")
altExp(es, subsetName = "hvg1000") <- es@subsets$hvg1000@internalAssay
expect_equal(length(altExpNames(es, subsetName = "hvg1000")), 2)
expect_true(!is.null(altExp(es, subsetName = "hvg1000")))
altExp(es) <- tenx_pbmc4k
expect_true(!is.null(altExp(es)))
altExp(es, "a1") <- tenx_pbmc4k
expect_true("a1" %in% altExpNames(es))
expect_true(!is.null(altExp(es, "a1")))
testthat::expect_error(altExpNames(es, subsetName = "na"),
"na subset does not exist.")
testthat::expect_error(altExpNames(es, subsetName = "na") <- c("na2"),
"na subset does not exist.")
altExpNames(es) <- c("a1", "a2")
expect_true(all.equal(altExpNames(es), c("a1", "a2")))
testthat::expect_error(altExp(es, "alt1", subsetName = "hvg10002"),
"hvg10002 subset does not exist.")
altExpNames(es, subsetName = "hvg1000") <- c("a1", "a2")
expect_true(all.equal(altExpNames(es, subsetName = "hvg1000"), c("a1", "a2")))
testthat::expect_error(altExpNames(es, subsetName = "hvg1000x"),
"hvg1000x subset does not exist.")
altExps(es, subsetName = "hvg1000") <- list(a = es@subsets$hvg1000@internalAssay, b = es@subsets$hvg1000@internalAssay)
expect_true(all.equal(altExpNames(es, subsetName = "hvg1000"), c("a","b")))
testthat::expect_error(altExps(es, subsetName = "hvg") <- list(a = es@subsets$hvg1000@internalAssay, b = es@subsets$hvg1000@internalAssay),
"hvg subset does not exist.")
testthat::expect_error(altExps(es, subsetName = "hvg10002"),
"hvg10002 subset does not exist.")
altExps(es) <- list(a = tenx_pbmc4k, b = tenx_pbmc4k)
expect_true(all.equal(altExpNames(es), c("a", "b")))
}
)
testthat::test_that("Testing createSubset with multiple paramter options",{
es <- ExperimentSubset(sce_chcl)
testthat::expect_error(es <- createSubset(es, "subset1", rows = c(10,11,50,56,98,99,102,105,109, 200), cols = c(20,21,40,45,90,99,100,123,166,299), parentAssay = "none"), "Input parentAssay does not exist.")
#colnames
es <- createSubset(es, "subset1", rows = c(10,11,50,56,98,99,102,105,109, 200), cols = c("CTGCTGTCAGGGTATG", "CAGTCCTTCGGTTAAC"), parentAssay = "counts")
testthat::expect_equal(es@subsets$subset1@subsetName, "subset1")
testthat::expect_equal(es@subsets$subset1@rowIndices, c(10,11,50,56,98,99,102,105,109, 200))
testthat::expect_equal(es@subsets$subset1@colIndices, match(c("CTGCTGTCAGGGTATG", "CAGTCCTTCGGTTAAC"), subsetColnames(es, subsetName = "subset1")))
testthat::expect_equal(es@subsets$subset1@parentAssay, "counts")
#null rows and null cols
es <- createSubset(es, "subset2", parentAssay = "counts")
testthat::expect_equal(es@subsets$subset2@subsetName, "subset2")
testthat::expect_equal(es@subsets$subset2@rowIndices, c(1:subsetDim(es, "subset2")[1]))
testthat::expect_equal(es@subsets$subset2@colIndices, c(1:subsetDim(es, "subset2")[2]))
testthat::expect_equal(es@subsets$subset2@parentAssay, "counts")
#nas introduced in rows or cols : update: this error is changed and does not appear in this way
# testthat::expect_error(es <- createSubset(es, "subset22", rows = c("as", "asd", "asd"), cols = c("CTGCTGTCAGGGTATG", "CAGTCCTTCGGTTAAC"), parentAssay = "counts"), "NAs introduced in input rows or columns. Some or all indicated rows or columns not found in specified parent.")
# testthat::expect_error(es <- createSubset(es, "subset22", cols = c("CTGTG", "CAGTCC"), parentAssay = "counts"), "NAs introduced in input rows or columns. Some or all indicated rows or columns not found in specified parent.")
})
testthat::test_that("Completing test coverage, move this into relevant places later",{
es <- ExperimentSubset(sce_chcl)
testthat::expect_warning(es <- createSubset(es, "subset 1", rows = c(1:5), cols = (1:5)),
"Removing spaces from the specified subsetName.")
es <- ExperimentSubset(list(counts = assay(sce_chcl, "counts")))
})
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