context("All-classes")
test_that("check that accessors output the expected result", {
expect_is(getData(CIMseqSinglets_test, "counts"), "matrix")
expect_is(getData(CIMseqSinglets_test, "counts.log"), "matrix")
expect_is(getData(CIMseqSinglets_test, "counts.cpm"), "matrix")
expect_is(getData(CIMseqSinglets_test, "counts.ercc"), "matrix")
expect_is(getData(CIMseqSinglets_test, "dim.red"), "matrix")
expect_is(getData(CIMseqSinglets_test, "classification"), "character")
expect_is(getData(CIMseqMultiplets_test, "counts"), "matrix")
expect_is(getData(CIMseqMultiplets_test, "counts.log"), "matrix")
expect_is(getData(CIMseqMultiplets_test, "counts.cpm"), "matrix")
expect_is(getData(CIMseqMultiplets_test, "counts.ercc"), "matrix")
expect_is(getData(CIMseqMultiplets_test, "features"), "integer")
expect_is(getData(CIMseqSwarm_test, "fractions"), "matrix")
expect_is(getData(CIMseqSwarm_test, "costs"), "numeric")
expect_is(getData(CIMseqSwarm_test, "convergence"), "character")
expect_is(getData(CIMseqSwarm_test, "stats"), "tbl_df")
expect_is(getData(CIMseqSwarm_test, "singletIdx"), "list")
expect_is(getData(CIMseqSwarm_test, "arguments"), "tbl_df")
})
test_that("check that replacement outputs the expected result", {
expect_error(getData(CIMseqSinglets_test, "counts") <- "a")
expect_error(getData(CIMseqSinglets_test, "counts.log") <- "a")
expect_error(getData(CIMseqSinglets_test, "counts.cpm") <- "a")
expect_error(getData(CIMseqSinglets_test, "counts.ercc") <- "a")
expect_error(getData(CIMseqSinglets_test, "dim.red") <- "a")
expect_error(getData(CIMseqSinglets_test, "classification") <- 1)
expect_error(getData(CIMseqMultiplets_test, "counts") <- "a")
expect_error(getData(CIMseqMultiplets_test, "counts.log") <- "a")
expect_error(getData(CIMseqMultiplets_test, "counts.cpm") <- "a")
expect_error(getData(CIMseqMultiplets_test, "counts.ercc") <- "a")
expect_error(getData(CIMseqMultiplets_test, "features") <- "a")
tmp <- CIMseqSinglets_test
getData(tmp, "counts") <- getData(CIMseqSinglets_test, "counts")
expect_is(tmp, "CIMseqSinglets")
tmp <- CIMseqSinglets_test
getData(tmp, "counts.log") <- function(){}
expect_is(tmp, "CIMseqSinglets")
tmp <- CIMseqSinglets_test
getData(tmp, "counts.cpm") <- function(){}
expect_is(tmp, "CIMseqSinglets")
tmp <- CIMseqSinglets_test
getData(tmp, "counts.ercc") <- getData(CIMseqSinglets_test, "counts.ercc")
expect_is(tmp, "CIMseqSinglets")
tmp <- CIMseqSinglets_test
getData(tmp, "dim.red") <- getData(CIMseqSinglets_test, "dim.red")
expect_is(tmp, "CIMseqSinglets")
tmp <- CIMseqSinglets_test
getData(tmp, "classification") <- getData(CIMseqSinglets_test, "classification")
expect_is(tmp, "CIMseqSinglets")
tmp <- CIMseqMultiplets_test
getData(tmp, "counts") <- getData(CIMseqMultiplets_test, "counts")
expect_is(tmp, "CIMseqMultiplets")
tmp <- CIMseqMultiplets_test
getData(tmp, "counts.log") <- function(){}
expect_is(tmp, "CIMseqMultiplets")
tmp <- CIMseqMultiplets_test
getData(tmp, "counts.cpm") <- function(){}
expect_is(tmp, "CIMseqMultiplets")
tmp <- CIMseqMultiplets_test
getData(tmp, "counts.ercc") <- getData(CIMseqMultiplets_test, "counts.ercc")
expect_is(tmp, "CIMseqMultiplets")
tmp <- CIMseqMultiplets_test
getData(tmp, "features") <- getData(CIMseqMultiplets_test, "features")
expect_is(tmp, "CIMseqMultiplets")
})
test_that("check that CIMseqSinglets concatenation outputs the expected result", {
#setup expected data
counts <- cbind(
getData(CIMseqSinglets_test, "counts"),
getData(CIMseqSinglets_test, "counts")
)
counts.ercc <- cbind(
getData(CIMseqSinglets_test, "counts.ercc"),
getData(CIMseqSinglets_test, "counts.ercc")
)
dim.red <- rbind(
getData(CIMseqSinglets_test, "dim.red"),
getData(CIMseqSinglets_test, "dim.red")
)
classification <- c(
getData(CIMseqSinglets_test, "classification"),
getData(CIMseqSinglets_test, "classification")
)
expected <- CIMseqSinglets(counts, counts.ercc, dim.red, classification)
#generate output
output <- c(CIMseqSinglets_test, CIMseqSinglets_test)
#test
expect_identical(getData(expected, "counts"), getData(output, "counts"))
expect_identical(getData(expected, "counts.log"), getData(output, "counts.log"))
expect_identical(getData(expected, "counts.cpm"), getData(output, "counts.cpm"))
expect_identical(getData(expected, "counts.ercc"), getData(output, "counts.ercc"))
expect_identical(getData(expected, "dim.red"), getData(output, "dim.red"))
expect_identical(getData(expected, "classification"), getData(output, "classification"))
#TEST, 2 if genes differ
CIMseqSinglets_test2 <- CIMseqSinglets(
getData(CIMseqSinglets_test, "counts")[1:100, ],
getData(CIMseqSinglets_test, "counts.ercc"),
getData(CIMseqSinglets_test, "dim.red"),
getData(CIMseqSinglets_test, "classification")
)
expect_error(c(CIMseqSinglets_test, CIMseqSinglets_test2))
#TEST 3, ERCC differ
CIMseqSinglets_test3 <- CIMseqSinglets(
getData(CIMseqSinglets_test, "counts"),
getData(CIMseqSinglets_test, "counts.ercc")[1:2, ],
getData(CIMseqSinglets_test, "dim.red"),
getData(CIMseqSinglets_test, "classification")
)
expect_error(c(CIMseqSinglets_test, CIMseqSinglets_test3))
#TEST 4, different dim.red
dr <- getData(CIMseqSinglets_test, "dim.red")
colnames(dr) <- c("dim1", "dim2")
CIMseqSinglets_test4 <- CIMseqSinglets(
getData(CIMseqSinglets_test, "counts"),
getData(CIMseqSinglets_test, "counts.ercc"),
dr,
getData(CIMseqSinglets_test, "classification")
)
expect_error(c(CIMseqSinglets_test, CIMseqSinglets_test4))
})
test_that("check that CIMseqMultiplets concatenation outputs the expected result", {
#setup expected data
counts <- cbind(
getData(CIMseqMultiplets_test, "counts"),
getData(CIMseqMultiplets_test, "counts")
)
counts.ercc <- cbind(
getData(CIMseqMultiplets_test, "counts.ercc"),
getData(CIMseqMultiplets_test, "counts.ercc")
)
features <- getData(CIMseqMultiplets_test, "features")
expected <- CIMseqMultiplets(counts, counts.ercc, features)
#generate output
output <- c(CIMseqMultiplets_test, CIMseqMultiplets_test)
#test
expect_identical(getData(expected, "counts"), getData(output, "counts"))
expect_identical(getData(expected, "counts.log"), getData(output, "counts.log"))
expect_identical(getData(expected, "counts.cpm"), getData(output, "counts.cpm"))
expect_identical(getData(expected, "counts.ercc"), getData(output, "counts.ercc"))
expect_identical(getData(expected, "features"), getData(output, "features"))
#TEST, 2 if genes differ
CIMseqMultiplets_test2 <- CIMseqMultiplets(
getData(CIMseqMultiplets_test, "counts")[1:100, ],
getData(CIMseqMultiplets_test, "counts.ercc"),
getData(CIMseqMultiplets_test, "features")
)
expect_error(c(CIMseqMultiplets_test, CIMseqMultiplets_test2))
#TEST 3, ERCC differ
CIMseqMultiplets_test3 <- CIMseqMultiplets(
getData(CIMseqMultiplets_test, "counts"),
getData(CIMseqMultiplets_test, "counts.ercc")[1:2, ],
getData(CIMseqMultiplets_test, "features")
)
expect_error(c(CIMseqMultiplets_test, CIMseqMultiplets_test3))
#TEST 4, different features
CIMseqMultiplets_test4 <- CIMseqMultiplets(
getData(CIMseqMultiplets_test, "counts"),
getData(CIMseqMultiplets_test, "counts.ercc"),
1:10
)
expect_warning(c(CIMseqMultiplets_test, CIMseqMultiplets_test4))
})
test_that("check that CIMseqSwarm concatenation outputs the expected result", {
#setup expected data
fractions <- rbind(
getData(CIMseqSwarm_test, "fractions"),
getData(CIMseqSwarm_test, "fractions")
)
costs <- c(
getData(CIMseqSwarm_test, "costs"),
getData(CIMseqSwarm_test, "costs")
)
convergence <- c(
getData(CIMseqSwarm_test, "convergence"),
getData(CIMseqSwarm_test, "convergence")
)
stats <- rbind(
getData(CIMseqSwarm_test, "stats"),
getData(CIMseqSwarm_test, "stats")
)
singletIdx <- c(getData(CIMseqSwarm_test, "singletIdx"))
arguments <- rbind(
getData(CIMseqSwarm_test, "arguments"),
getData(CIMseqSwarm_test, "arguments")
)
expected <- new("CIMseqSwarm",
fractions = fractions, costs = costs, convergence = convergence,
stats = stats, singletIdx = singletIdx, arguments = arguments
)
#generate output
output <- c(CIMseqSwarm_test, CIMseqSwarm_test)
#test
expect_identical(getData(expected, "fractions"), getData(output, "fractions"))
expect_identical(getData(expected, "costs"), getData(output, "costs"))
expect_identical(getData(expected, "convergence"), getData(output, "convergence"))
expect_identical(getData(expected, "stats"), getData(output, "stats"))
expect_identical(getData(expected, "singletIdx"), getData(output, "singletIdx"))
expect_identical(getData(expected, "arguments"), getData(output, "arguments"))
#TEST 2, non-matching classes
f <- getData(CIMseqSwarm_test, "fractions")
colnames(f) <- paste0("c", 1:ncol(f))
CIMseqSwarm_test2 <- new(
"CIMseqSwarm",
fractions = f,
costs = getData(CIMseqSwarm_test, "costs"),
convergence = getData(CIMseqSwarm_test, "convergence"),
stats = getData(CIMseqSwarm_test, "stats"),
singletIdx = getData(CIMseqSwarm_test, "singletIdx"),
arguments = getData(CIMseqSwarm_test, "arguments")
)
expect_error(c(CIMseqSwarm_test, CIMseqSwarm_test2))
#TEST 3; non-matching singletIdx
CIMseqSwarm_test3 <- new(
"CIMseqSwarm",
fractions = getData(CIMseqSwarm_test, "fractions"),
costs = getData(CIMseqSwarm_test, "costs"),
convergence = getData(CIMseqSwarm_test, "convergence"),
stats = getData(CIMseqSwarm_test, "stats"),
singletIdx = getData(CIMseqSwarm_test, "singletIdx")[1:200],
arguments = getData(CIMseqSwarm_test, "arguments")
)
expect_warning(c(CIMseqSwarm_test, CIMseqSwarm_test3))
})
test_that("check that CIMseqSwarm subsetting outputs the expected result", {
#setup expected data
s <- c("m.NJB00204.G04", "m.NJB00204.D07")
fractions <- getData(CIMseqSwarm_test, "fractions")[s, ]
costs <- getData(CIMseqSwarm_test, "costs")[s]
convergence <- getData(CIMseqSwarm_test, "convergence")[s]
stats <- filter(getData(CIMseqSwarm_test, "stats"), sample %in% s)
singletIdx <- getData(CIMseqSwarm_test, "singletIdx")
arguments <- getData(CIMseqSwarm_test, "arguments")
expected <- new(
"CIMseqSwarm",
fractions = fractions, costs = costs, convergence = convergence,
stats = stats, singletIdx = singletIdx, arguments = arguments
)
#generate output
output <- filterSwarm(CIMseqSwarm_test, s)
#test
expect_identical(getData(expected, "fractions"), getData(output, "fractions"))
expect_identical(getData(expected, "costs"), getData(output, "costs"))
expect_identical(getData(expected, "convergence"), getData(output, "convergence"))
expect_identical(getData(expected, "stats"), getData(output, "stats"))
expect_identical(getData(expected, "singletIdx"), getData(output, "singletIdx"))
expect_identical(getData(expected, "arguments"), getData(output, "arguments"))
})
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