tests/testthat/test_constructors.R
In markrobinsonuzh/iCOBRA: Comparison and Visualization of Ranking and Assignment Methods
## Test that the constructors generate objects of the correct type
library(iCOBRA)
context("Check that constructors generate objects of the correct type")
test_that("COBRAData constructors generate COBRAData objects", {
expect_is(COBRAData(), "COBRAData")
expect_is(COBRAData_from_text(
truth_file = system.file("extdata", "cobradata_example_truth.txt",
package = "iCOBRA"),
result_files = system.file("extdata", "cobradata_example_results_4.txt",
package = "iCOBRA"),
feature_id = "feature"), "COBRAData")
expect_is(COBRAData_from_text(
truth_file = system.file("extdata", "cobradata_example_truth.txt",
package = "iCOBRA"),
result_files = system.file("extdata", "cobradata_example_results_2.txt",
package = "iCOBRA"),
feature_id = "feature"), "COBRAData")
ibt <- COBRAData_from_text(
truth_file = system.file("extdata", "cobradata_example_truth.txt",
package = "iCOBRA"),
result_files = system.file("extdata", "cobradata_example_results_3.txt",
package = "iCOBRA"),
feature_id = "feature")
expect_is(ibt, "COBRAData")
expect_equal(length(pval(ibt)), 0)
expect_equal(length(padj(ibt)), 0)
expect_equal(length(score(ibt)), 0)
pval <- c(0.0058, 0.771, 0.024, 0.741, 0.247)
padj <- p.adjust(pval, method = "BH")
score <- 1:5
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = paste0("F", 1:5)),
padj = data.frame(m1 = padj, row.names = paste0("F", 1:5)),
score = data.frame(m1 = score, row.names = paste0("F", 1:5)),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = paste0("F", 1:5)))
ib2 <- COBRAData(pval = data.frame(m2 = pval, row.names = paste0("F", 1:5)),
padj = data.frame(m2 = padj, row.names = paste0("F", 1:5)),
score = data.frame(m2 = score, row.names = paste0("F", 1:5)),
object_to_extend = ib)
expect_equal(pval(ib2)$m1, pval(ib2)$m2)
expect_equal(padj(ib2)$m1, padj(ib2)$m2)
expect_equal(score(ib2)$m1, score(ib2)$m2)
})
test_that("extending empty COBRAData object works as expected", {
ibA <- COBRAData(pval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
padj = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
sval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
score = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
truth = data.frame(status = c(1, 0, 1, 0, 1),
row.names = paste0("F", 1:5)))
ibB <- COBRAData()
ibC <- COBRAData(pval = pval(ibA), padj = padj(ibA), sval = sval(ibA),
score = score(ibA), truth = truth(ibA),
object_to_extend = ibB)
expect_equal(pval(ibA), pval(ibC))
expect_equal(padj(ibA), padj(ibC))
expect_equal(sval(ibA), sval(ibC))
expect_equal(score(ibA), score(ibC))
expect_equal(truth(ibA), truth(ibC))
})
test_that("extending object with object without pval slot works", {
ibA <- COBRAData(pval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
padj = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
sval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
score = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
truth = data.frame(status = c(1, 0, 1, 0, 1),
row.names = paste0("F", 1:5)))
ibB <- COBRAData(score = score(ibA),
object_to_extend = ibA)
expect_equal(pval(ibA), pval(ibB))
expect_equal(padj(ibA), padj(ibB))
expect_equal(sval(ibA), sval(ibB))
expect_equal(score(ibA), score(ibB))
expect_equal(truth(ibA), truth(ibB))
})
test_that("extending COBRAData objects works as expected", {
ibA <- COBRAData(pval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
padj = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
score = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
truth = data.frame(status = c(1, 0, 1, 0, 1),
row.names = paste0("F", 1:5)))
ibAp <- ibA
truth(ibAp)$expr <- 1:5
truth(ibAp)$status <- c(0, 1, 0, 1, 0)
ibB <- COBRAData(pval = data.frame(mB = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6),
row.names = paste0("F", 1:6)),
padj = data.frame(mA = c(0.6, 0.7, 0.8, 0.9, 1.0),
row.names = paste0("F", 1:5)),
sval = data.frame(mA = c(0.6, 0.7, 0.8, 0.9, 1.0),
row.names = paste0("F", 1:5)),
score = data.frame(mB = c(0.6, 0.7, 0.8),
row.names = paste0("F", 1:3)),
truth = data.frame(status = c(1, 0, 1, 0, 1, 0),
expr = 1:6,
row.names = paste0("F", 1:6)))
ibBp <- ibB
truth(ibBp)$expr <- NULL
truth(ibBp)$status <- c(0, 1, 0, 1, 0, 1)
ibtest <- COBRAData(pval = pval(ibA), padj = padj(ibA), score = score(ibA),
sval = sval(ibA), truth = truth(ibA), object_to_extend = ibB)
expect_equal(nrow(pval(ibtest)), 6)
expect_equal(pval(ibtest)[paste0("F", 1:6), "mB"], c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6))
expect_equal(nrow(padj(ibtest)), 5)
expect_equal(ncol(padj(ibtest)), 1)
expect_equal(padj(ibtest)[paste0("F", 1:5), "mA"], c(0.6, 0.7, 0.8, 0.9, 1.0))
expect_equal(sval(ibtest)[paste0("F", 1:5), "mA"], c(0.6, 0.7, 0.8, 0.9, 1.0))
expect_equal(score(ibtest)[paste0("F", 1:5), "mB"], c(0.6, 0.7, 0.8, NA, NA))
expect_equal(truth(ibtest)[paste0("F", 1:6), "expr"], 1:6)
expect_equal(ncol(truth(ibtest)), 2)
expect_error(COBRAData(pval = pval(ibA), padj = padj(ibA), score = score(ibA),
sval = sval(ibA), truth = truth(ibA), object_to_extend = ibBp))
ibtestp <- COBRAData(pval = pval(ibBp), padj = padj(ibBp), score = score(ibBp),
sval = sval(ibBp), truth = truth(ibBp), object_to_extend = ibAp)
expect_equal(pval(ibtest)[paste0("F", 1:6), c("mA", "mB")],
pval(ibtestp)[paste0("F", 1:6), c("mA", "mB")])
expect_equal(padj(ibtestp)[paste0("F", 1:5), "mA"], c(0.1, 0.2, 0.3, 0.4, 0.5))
expect_equal(score(ibtest)[paste0("F", 1:5), c("mA", "mB")],
score(ibtestp)[paste0("F", 1:5), c("mA", "mB")])
expect_equal(truth(ibtestp)[paste0("F", 1:6), "expr"], c(1:5, NA))
})
test_that("export functions return correct class", {
expect_is(COBRAData_to_text(cobradata_example_sval, feature_id = "feature",
truth_file = "test_truth.txt",
result_files = "test_results.txt"), "NULL")
})
test_that(paste0("COBRAPerformance constructor and calculate_performance ",
"generate COBRAPerformance objects"), {
expect_is(COBRAPerformance(), "COBRAPerformance")
expect_is(calculate_performance(cobradata_example_sval,
binary_truth = "status",
aspects = "fpr"),
"COBRAPerformance")
ip <- COBRAPerformance()
onlyshared(ip) <- TRUE
expect_is(ip, "COBRAPerformance")
})
test_that(paste0("COBRAPlot constructor and prepare_data_for_plot ",
"generate COBRAPlot objects"), {
expect_is(COBRAPlot(), "COBRAPlot")
expect_is(
prepare_data_for_plot(
calculate_performance(cobradata_example_sval,
binary_truth = "status",
aspects = "fpr")), "COBRAPlot")
})
test_that("replacement still returns valid objects", {
cobradata <- cobradata_example_sval
pval(cobradata) <- pval(cobradata)[1:500, ]
padj(cobradata) <- padj(cobradata)[1:1000, ]
sval(cobradata) <- sval(cobradata)[1:1000, ]
score(cobradata) <- score(cobradata)[1:750, ]
truth(cobradata) <- truth(cobradata)[1:500, ]
expect_is(cobradata, "COBRAData")
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC")
fdrtpr(cobraperf) <- fdrtpr(cobraperf)[1:2, ]
fdrtprcurve(cobraperf) <- fdrtprcurve(cobraperf)[1:2, ]
fdrnbr(cobraperf) <- fdrnbr(cobraperf)[1:2, ]
fdrnbrcurve(cobraperf) <- fdrnbrcurve(cobraperf)[1:2, ]
fsrnbr(cobraperf) <- fsrnbr(cobraperf)[1:2, ]
fsrnbrcurve(cobraperf) <- fsrnbrcurve(cobraperf)[1:2, ]
fpr(cobraperf) <- fpr(cobraperf)[1:2, ]
tpr(cobraperf) <- tpr(cobraperf)[1:2, ]
roc(cobraperf) <- roc(cobraperf)[1:2, ]
fpc(cobraperf) <- fpc(cobraperf)[1:2, ]
deviation(cobraperf) <- deviation(cobraperf)[1:2, ]
scatter(cobraperf) <- scatter(cobraperf)[1:2, ]
fdrtpr(cobraperf) <- fdrtpr(cobraperf)[1:2, ]
overlap(cobraperf) <- overlap(cobraperf)[1:2, ]
corr(cobraperf) <- corr(cobraperf)[1:2, ]
maxsplit(cobraperf) <- 4
splv(cobraperf) <- "none"
expect_is(cobraperf, "COBRAPerformance")
cobraplot <- prepare_data_for_plot(cobraperf)
plotcolors(cobraplot) <- plotcolors(cobraplot)[1:5]
facetted(cobraplot) <- FALSE
expect_true(iCOBRA:::is_plottable(tpr(cobraplot)))
fdrtpr(cobraplot) <- fdrtpr(cobraplot)[1:2, ]
fdrtprcurve(cobraplot) <- fdrtprcurve(cobraplot)[1:2, ]
fdrnbr(cobraplot) <- fdrnbr(cobraplot)[1:2, ]
fdrnbrcurve(cobraplot) <- fdrnbrcurve(cobraplot)[1:2, ]
fsrnbr(cobraplot) <- fsrnbr(cobraplot)[1:2, ]
fsrnbrcurve(cobraplot) <- fsrnbrcurve(cobraplot)[1:2, ]
fpr(cobraplot) <- fpr(cobraplot)[1:2, ]
tpr(cobraplot) <- tpr(cobraplot)[1:2, ]
roc(cobraplot) <- roc(cobraplot)[1:2, ]
fpc(cobraplot) <- fpc(cobraplot)[1:2, ]
deviation(cobraplot) <- deviation(cobraplot)[1:2, ]
scatter(cobraplot) <- scatter(cobraplot)[1:2, ]
fdrtpr(cobraplot) <- fdrtpr(cobraplot)[1:2, ]
overlap(cobraplot) <- overlap(cobraplot)[1:2, ]
corr(cobraplot) <- corr(cobraplot)[1:2, ]
maxsplit(cobraplot) <- 4
splv(cobraplot) <- "none"
onlyshared(cobraplot) <- TRUE
expect_is(cobraplot, "COBRAPlot")
})
test_that("show returns NULL", {
cobradata <- cobradata_example_sval
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "tpr")
cobraperf2 <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC",
aspects = c("tpr", "overlap"),
splv = "expr_cat", maxsplit = 4)
cobraplot <- prepare_data_for_plot(cobraperf2, colorscheme = "Set3",
facetted = FALSE)
expect_is(show(cobradata), "NULL")
expect_is(show(cobraperf), "NULL")
expect_is(show(cobraperf2), "NULL")
expect_is(show(cobraplot), "NULL")
})
test_that("subsetting of objects works", {
cobradata <- cobradata_example_sval
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "tpr")
cobraplot <- prepare_data_for_plot(cobraperf)
expect_error(cobraplot[, "nonexisting_method"])
expect_is(cobraplot[, "Method2"], "COBRAPlot")
expect_equal(tpr(cobraplot[, "Method2"])$basemethod, rep("Method2", 3))
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "overlap",
splv = "none")
cobraplot <- prepare_data_for_plot(cobraperf)
expect_error(cobraperf[, "nonexisting_method"])
expect_is(overlap(cobraperf[, "Method2"]), "data.frame")
expect_is(overlap(cobraplot[, "Method2"]), "data.frame")
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "overlap",
splv = "expr_cat")
cobraplot <- prepare_data_for_plot(cobraperf)
expect_error(cobraperf[, "nonexisting_method"])
expect_is(cobraperf[, "Method2"], "COBRAPerformance")
expect_is(overlap(cobraperf[, "Method2"]), "list")
expect_equal(colnames(overlap(cobraperf[, "Method2"])[[1]]), c("Method2", "truth"))
expect_error(cobraplot[, "nonexisting_method"])
expect_is(cobraplot[, "Method2"], "COBRAPlot")
expect_is(overlap(cobraplot[, "Method2"]), "list")
expect_equal(colnames(overlap(cobraplot[, "Method2"])[[1]]), c("Method2", "truth"))
kp <- rownames(pval(cobradata))[1:50]
expect_error(cobradata["nonexisting_variable", ])
expect_is(cobradata[kp, ], "COBRAData")
expect_error(cobraplot[kp, ])
expect_equal(nrow(pval(cobradata[kp, ])), length(kp))
})
test_that("extending an object still returns valid objects", {
cobradata <- cobradata_example_sval
cobradata <- COBRAData(pval = pval(cobradata), object_to_extend = cobradata)
cobradata <- COBRAData(sval = sval(cobradata), object_to_extend = cobradata)
expect_is(cobradata, "COBRAData")
})
test_that("extending an object of the wrong class doesn't work", {
cobradata <- cobradata_example_sval
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "tpr")
expect_error(COBRAData(pval = pval(cobradata), object_to_extend = cobraperf))
})
test_that("updating COBRAData object works", {
expect_warning({
expect_is(sval(cobradata_example), "data.frame")
}, "Object doesn't have a slot sval")
cobradata <- update_cobradata(cobradata_example)
expect_is(cobradata, "COBRAData")
expect_is(cobradata@sval, "data.frame")
})
test_that("updating COBRAPerformance object works", {
cobradata <- cobradata_example_sval
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "tpr")
expect_is(fsrnbr(cobraperf), "data.frame")
cobraperf <- update_cobraperformance(cobraperf)
expect_is(cobraperf, "COBRAPerformance")
})
test_that("reordering levels in COBRAPlot object works", {
cobraperf <- calculate_performance(calculate_adjp(cobradata_example_sval),
binary_truth = "status", aspects = "fpr")
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
incltruth = TRUE)
cobraplot <- reorder_levels(cobraplot, c("Method3", "Method1"))
expect_is(cobraplot, "COBRAPlot")
expect_equal(levels(fpr(cobraplot)$method), c("Method3", "Method1", "Method2"))
})
test_that("creating objects from data frames without row names generates warning", {
pval <- c(0.0058, 0.771, 0.024, 0.741, 0.247)
padj <- p.adjust(pval, method = "BH")
score <- 1:5
expect_warning({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = NULL),
padj = data.frame(m1 = padj, row.names = NULL),
score = data.frame(m1 = score, row.names = NULL),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = NULL))
})
})
test_that(paste0("creating objects from data frames with mixed present/missing",
"row names generates error"), {
pval <- c(0.0058, 0.771, 0.024, 0.741, 0.247)
padj <- p.adjust(pval, method = "BH")
score <- 1:5
expect_error({
suppressWarnings({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = paste0("F", 1:5)),
padj = data.frame(m1 = padj, row.names = NULL),
score = data.frame(m1 = score, row.names = NULL),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = NULL))
})
})
expect_error({
suppressWarnings({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = NULL),
padj = data.frame(m1 = padj, row.names = paste0("F", 1:5)),
score = data.frame(m1 = score, row.names = NULL),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = NULL))
})
})
expect_error({
suppressWarnings({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = NULL),
padj = data.frame(m1 = padj, row.names = NULL),
score = data.frame(m1 = score, row.names = paste0("F", 1:5)),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = NULL))
})
})
expect_error({
suppressWarnings({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = NULL),
padj = data.frame(m1 = padj, row.names = NULL),
score = data.frame(m1 = score, row.names = NULL),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = paste0("F", 1:5)))
})
})
})
markrobinsonuzh/iCOBRA documentation built on March 28, 2024, 2:01 p.m.
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## Test that the constructors generate objects of the correct type
library(iCOBRA)
context("Check that constructors generate objects of the correct type")
test_that("COBRAData constructors generate COBRAData objects", {
expect_is(COBRAData(), "COBRAData")
expect_is(COBRAData_from_text(
truth_file = system.file("extdata", "cobradata_example_truth.txt",
package = "iCOBRA"),
result_files = system.file("extdata", "cobradata_example_results_4.txt",
package = "iCOBRA"),
feature_id = "feature"), "COBRAData")
expect_is(COBRAData_from_text(
truth_file = system.file("extdata", "cobradata_example_truth.txt",
package = "iCOBRA"),
result_files = system.file("extdata", "cobradata_example_results_2.txt",
package = "iCOBRA"),
feature_id = "feature"), "COBRAData")
ibt <- COBRAData_from_text(
truth_file = system.file("extdata", "cobradata_example_truth.txt",
package = "iCOBRA"),
result_files = system.file("extdata", "cobradata_example_results_3.txt",
package = "iCOBRA"),
feature_id = "feature")
expect_is(ibt, "COBRAData")
expect_equal(length(pval(ibt)), 0)
expect_equal(length(padj(ibt)), 0)
expect_equal(length(score(ibt)), 0)
pval <- c(0.0058, 0.771, 0.024, 0.741, 0.247)
padj <- p.adjust(pval, method = "BH")
score <- 1:5
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = paste0("F", 1:5)),
padj = data.frame(m1 = padj, row.names = paste0("F", 1:5)),
score = data.frame(m1 = score, row.names = paste0("F", 1:5)),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = paste0("F", 1:5)))
ib2 <- COBRAData(pval = data.frame(m2 = pval, row.names = paste0("F", 1:5)),
padj = data.frame(m2 = padj, row.names = paste0("F", 1:5)),
score = data.frame(m2 = score, row.names = paste0("F", 1:5)),
object_to_extend = ib)
expect_equal(pval(ib2)$m1, pval(ib2)$m2)
expect_equal(padj(ib2)$m1, padj(ib2)$m2)
expect_equal(score(ib2)$m1, score(ib2)$m2)
})
test_that("extending empty COBRAData object works as expected", {
ibA <- COBRAData(pval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
padj = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
sval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
score = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
truth = data.frame(status = c(1, 0, 1, 0, 1),
row.names = paste0("F", 1:5)))
ibB <- COBRAData()
ibC <- COBRAData(pval = pval(ibA), padj = padj(ibA), sval = sval(ibA),
score = score(ibA), truth = truth(ibA),
object_to_extend = ibB)
expect_equal(pval(ibA), pval(ibC))
expect_equal(padj(ibA), padj(ibC))
expect_equal(sval(ibA), sval(ibC))
expect_equal(score(ibA), score(ibC))
expect_equal(truth(ibA), truth(ibC))
})
test_that("extending object with object without pval slot works", {
ibA <- COBRAData(pval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
padj = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
sval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
score = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
truth = data.frame(status = c(1, 0, 1, 0, 1),
row.names = paste0("F", 1:5)))
ibB <- COBRAData(score = score(ibA),
object_to_extend = ibA)
expect_equal(pval(ibA), pval(ibB))
expect_equal(padj(ibA), padj(ibB))
expect_equal(sval(ibA), sval(ibB))
expect_equal(score(ibA), score(ibB))
expect_equal(truth(ibA), truth(ibB))
})
test_that("extending COBRAData objects works as expected", {
ibA <- COBRAData(pval = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
padj = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
score = data.frame(mA = c(0.1, 0.2, 0.3, 0.4, 0.5),
row.names = paste0("F", 1:5)),
truth = data.frame(status = c(1, 0, 1, 0, 1),
row.names = paste0("F", 1:5)))
ibAp <- ibA
truth(ibAp)$expr <- 1:5
truth(ibAp)$status <- c(0, 1, 0, 1, 0)
ibB <- COBRAData(pval = data.frame(mB = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6),
row.names = paste0("F", 1:6)),
padj = data.frame(mA = c(0.6, 0.7, 0.8, 0.9, 1.0),
row.names = paste0("F", 1:5)),
sval = data.frame(mA = c(0.6, 0.7, 0.8, 0.9, 1.0),
row.names = paste0("F", 1:5)),
score = data.frame(mB = c(0.6, 0.7, 0.8),
row.names = paste0("F", 1:3)),
truth = data.frame(status = c(1, 0, 1, 0, 1, 0),
expr = 1:6,
row.names = paste0("F", 1:6)))
ibBp <- ibB
truth(ibBp)$expr <- NULL
truth(ibBp)$status <- c(0, 1, 0, 1, 0, 1)
ibtest <- COBRAData(pval = pval(ibA), padj = padj(ibA), score = score(ibA),
sval = sval(ibA), truth = truth(ibA), object_to_extend = ibB)
expect_equal(nrow(pval(ibtest)), 6)
expect_equal(pval(ibtest)[paste0("F", 1:6), "mB"], c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6))
expect_equal(nrow(padj(ibtest)), 5)
expect_equal(ncol(padj(ibtest)), 1)
expect_equal(padj(ibtest)[paste0("F", 1:5), "mA"], c(0.6, 0.7, 0.8, 0.9, 1.0))
expect_equal(sval(ibtest)[paste0("F", 1:5), "mA"], c(0.6, 0.7, 0.8, 0.9, 1.0))
expect_equal(score(ibtest)[paste0("F", 1:5), "mB"], c(0.6, 0.7, 0.8, NA, NA))
expect_equal(truth(ibtest)[paste0("F", 1:6), "expr"], 1:6)
expect_equal(ncol(truth(ibtest)), 2)
expect_error(COBRAData(pval = pval(ibA), padj = padj(ibA), score = score(ibA),
sval = sval(ibA), truth = truth(ibA), object_to_extend = ibBp))
ibtestp <- COBRAData(pval = pval(ibBp), padj = padj(ibBp), score = score(ibBp),
sval = sval(ibBp), truth = truth(ibBp), object_to_extend = ibAp)
expect_equal(pval(ibtest)[paste0("F", 1:6), c("mA", "mB")],
pval(ibtestp)[paste0("F", 1:6), c("mA", "mB")])
expect_equal(padj(ibtestp)[paste0("F", 1:5), "mA"], c(0.1, 0.2, 0.3, 0.4, 0.5))
expect_equal(score(ibtest)[paste0("F", 1:5), c("mA", "mB")],
score(ibtestp)[paste0("F", 1:5), c("mA", "mB")])
expect_equal(truth(ibtestp)[paste0("F", 1:6), "expr"], c(1:5, NA))
})
test_that("export functions return correct class", {
expect_is(COBRAData_to_text(cobradata_example_sval, feature_id = "feature",
truth_file = "test_truth.txt",
result_files = "test_results.txt"), "NULL")
})
test_that(paste0("COBRAPerformance constructor and calculate_performance ",
"generate COBRAPerformance objects"), {
expect_is(COBRAPerformance(), "COBRAPerformance")
expect_is(calculate_performance(cobradata_example_sval,
binary_truth = "status",
aspects = "fpr"),
"COBRAPerformance")
ip <- COBRAPerformance()
onlyshared(ip) <- TRUE
expect_is(ip, "COBRAPerformance")
})
test_that(paste0("COBRAPlot constructor and prepare_data_for_plot ",
"generate COBRAPlot objects"), {
expect_is(COBRAPlot(), "COBRAPlot")
expect_is(
prepare_data_for_plot(
calculate_performance(cobradata_example_sval,
binary_truth = "status",
aspects = "fpr")), "COBRAPlot")
})
test_that("replacement still returns valid objects", {
cobradata <- cobradata_example_sval
pval(cobradata) <- pval(cobradata)[1:500, ]
padj(cobradata) <- padj(cobradata)[1:1000, ]
sval(cobradata) <- sval(cobradata)[1:1000, ]
score(cobradata) <- score(cobradata)[1:750, ]
truth(cobradata) <- truth(cobradata)[1:500, ]
expect_is(cobradata, "COBRAData")
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC")
fdrtpr(cobraperf) <- fdrtpr(cobraperf)[1:2, ]
fdrtprcurve(cobraperf) <- fdrtprcurve(cobraperf)[1:2, ]
fdrnbr(cobraperf) <- fdrnbr(cobraperf)[1:2, ]
fdrnbrcurve(cobraperf) <- fdrnbrcurve(cobraperf)[1:2, ]
fsrnbr(cobraperf) <- fsrnbr(cobraperf)[1:2, ]
fsrnbrcurve(cobraperf) <- fsrnbrcurve(cobraperf)[1:2, ]
fpr(cobraperf) <- fpr(cobraperf)[1:2, ]
tpr(cobraperf) <- tpr(cobraperf)[1:2, ]
roc(cobraperf) <- roc(cobraperf)[1:2, ]
fpc(cobraperf) <- fpc(cobraperf)[1:2, ]
deviation(cobraperf) <- deviation(cobraperf)[1:2, ]
scatter(cobraperf) <- scatter(cobraperf)[1:2, ]
fdrtpr(cobraperf) <- fdrtpr(cobraperf)[1:2, ]
overlap(cobraperf) <- overlap(cobraperf)[1:2, ]
corr(cobraperf) <- corr(cobraperf)[1:2, ]
maxsplit(cobraperf) <- 4
splv(cobraperf) <- "none"
expect_is(cobraperf, "COBRAPerformance")
cobraplot <- prepare_data_for_plot(cobraperf)
plotcolors(cobraplot) <- plotcolors(cobraplot)[1:5]
facetted(cobraplot) <- FALSE
expect_true(iCOBRA:::is_plottable(tpr(cobraplot)))
fdrtpr(cobraplot) <- fdrtpr(cobraplot)[1:2, ]
fdrtprcurve(cobraplot) <- fdrtprcurve(cobraplot)[1:2, ]
fdrnbr(cobraplot) <- fdrnbr(cobraplot)[1:2, ]
fdrnbrcurve(cobraplot) <- fdrnbrcurve(cobraplot)[1:2, ]
fsrnbr(cobraplot) <- fsrnbr(cobraplot)[1:2, ]
fsrnbrcurve(cobraplot) <- fsrnbrcurve(cobraplot)[1:2, ]
fpr(cobraplot) <- fpr(cobraplot)[1:2, ]
tpr(cobraplot) <- tpr(cobraplot)[1:2, ]
roc(cobraplot) <- roc(cobraplot)[1:2, ]
fpc(cobraplot) <- fpc(cobraplot)[1:2, ]
deviation(cobraplot) <- deviation(cobraplot)[1:2, ]
scatter(cobraplot) <- scatter(cobraplot)[1:2, ]
fdrtpr(cobraplot) <- fdrtpr(cobraplot)[1:2, ]
overlap(cobraplot) <- overlap(cobraplot)[1:2, ]
corr(cobraplot) <- corr(cobraplot)[1:2, ]
maxsplit(cobraplot) <- 4
splv(cobraplot) <- "none"
onlyshared(cobraplot) <- TRUE
expect_is(cobraplot, "COBRAPlot")
})
test_that("show returns NULL", {
cobradata <- cobradata_example_sval
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "tpr")
cobraperf2 <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC",
aspects = c("tpr", "overlap"),
splv = "expr_cat", maxsplit = 4)
cobraplot <- prepare_data_for_plot(cobraperf2, colorscheme = "Set3",
facetted = FALSE)
expect_is(show(cobradata), "NULL")
expect_is(show(cobraperf), "NULL")
expect_is(show(cobraperf2), "NULL")
expect_is(show(cobraplot), "NULL")
})
test_that("subsetting of objects works", {
cobradata <- cobradata_example_sval
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "tpr")
cobraplot <- prepare_data_for_plot(cobraperf)
expect_error(cobraplot[, "nonexisting_method"])
expect_is(cobraplot[, "Method2"], "COBRAPlot")
expect_equal(tpr(cobraplot[, "Method2"])$basemethod, rep("Method2", 3))
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "overlap",
splv = "none")
cobraplot <- prepare_data_for_plot(cobraperf)
expect_error(cobraperf[, "nonexisting_method"])
expect_is(overlap(cobraperf[, "Method2"]), "data.frame")
expect_is(overlap(cobraplot[, "Method2"]), "data.frame")
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "overlap",
splv = "expr_cat")
cobraplot <- prepare_data_for_plot(cobraperf)
expect_error(cobraperf[, "nonexisting_method"])
expect_is(cobraperf[, "Method2"], "COBRAPerformance")
expect_is(overlap(cobraperf[, "Method2"]), "list")
expect_equal(colnames(overlap(cobraperf[, "Method2"])[[1]]), c("Method2", "truth"))
expect_error(cobraplot[, "nonexisting_method"])
expect_is(cobraplot[, "Method2"], "COBRAPlot")
expect_is(overlap(cobraplot[, "Method2"]), "list")
expect_equal(colnames(overlap(cobraplot[, "Method2"])[[1]]), c("Method2", "truth"))
kp <- rownames(pval(cobradata))[1:50]
expect_error(cobradata["nonexisting_variable", ])
expect_is(cobradata[kp, ], "COBRAData")
expect_error(cobraplot[kp, ])
expect_equal(nrow(pval(cobradata[kp, ])), length(kp))
})
test_that("extending an object still returns valid objects", {
cobradata <- cobradata_example_sval
cobradata <- COBRAData(pval = pval(cobradata), object_to_extend = cobradata)
cobradata <- COBRAData(sval = sval(cobradata), object_to_extend = cobradata)
expect_is(cobradata, "COBRAData")
})
test_that("extending an object of the wrong class doesn't work", {
cobradata <- cobradata_example_sval
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "tpr")
expect_error(COBRAData(pval = pval(cobradata), object_to_extend = cobraperf))
})
test_that("updating COBRAData object works", {
expect_warning({
expect_is(sval(cobradata_example), "data.frame")
}, "Object doesn't have a slot sval")
cobradata <- update_cobradata(cobradata_example)
expect_is(cobradata, "COBRAData")
expect_is(cobradata@sval, "data.frame")
})
test_that("updating COBRAPerformance object works", {
cobradata <- cobradata_example_sval
cobraperf <- calculate_performance(cobradata, binary_truth = "status",
cont_truth = "logFC", aspects = "tpr")
expect_is(fsrnbr(cobraperf), "data.frame")
cobraperf <- update_cobraperformance(cobraperf)
expect_is(cobraperf, "COBRAPerformance")
})
test_that("reordering levels in COBRAPlot object works", {
cobraperf <- calculate_performance(calculate_adjp(cobradata_example_sval),
binary_truth = "status", aspects = "fpr")
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
incltruth = TRUE)
cobraplot <- reorder_levels(cobraplot, c("Method3", "Method1"))
expect_is(cobraplot, "COBRAPlot")
expect_equal(levels(fpr(cobraplot)$method), c("Method3", "Method1", "Method2"))
})
test_that("creating objects from data frames without row names generates warning", {
pval <- c(0.0058, 0.771, 0.024, 0.741, 0.247)
padj <- p.adjust(pval, method = "BH")
score <- 1:5
expect_warning({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = NULL),
padj = data.frame(m1 = padj, row.names = NULL),
score = data.frame(m1 = score, row.names = NULL),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = NULL))
})
})
test_that(paste0("creating objects from data frames with mixed present/missing",
"row names generates error"), {
pval <- c(0.0058, 0.771, 0.024, 0.741, 0.247)
padj <- p.adjust(pval, method = "BH")
score <- 1:5
expect_error({
suppressWarnings({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = paste0("F", 1:5)),
padj = data.frame(m1 = padj, row.names = NULL),
score = data.frame(m1 = score, row.names = NULL),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = NULL))
})
})
expect_error({
suppressWarnings({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = NULL),
padj = data.frame(m1 = padj, row.names = paste0("F", 1:5)),
score = data.frame(m1 = score, row.names = NULL),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = NULL))
})
})
expect_error({
suppressWarnings({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = NULL),
padj = data.frame(m1 = padj, row.names = NULL),
score = data.frame(m1 = score, row.names = paste0("F", 1:5)),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = NULL))
})
})
expect_error({
suppressWarnings({
ib <- COBRAData(pval = data.frame(m1 = pval, row.names = NULL),
padj = data.frame(m1 = padj, row.names = NULL),
score = data.frame(m1 = score, row.names = NULL),
truth = data.frame(status = c(0, 1, 0, 1, 0),
row.names = paste0("F", 1:5)))
})
})
})
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