Nothing
library(Racmacs)
library(testthat)
context("Test local map creation")
# Set test table
testtable <- matrix(2 ^ (1:6) * 10, 6, 4)
# Backwards compatibility
test_that("table argument still works", {
# Making a map from a table
expect_warning({
map <- acmap(
table = testtable
)
}, "Argument 'table' is deprecated, please use 'titer_table' instead")
expect_equal(numAntigens(map), 6)
expect_equal(numSera(map), 4)
})
# Bare bones creation
test_that("Bare bones creation", {
# Making a map from a table
actablemap <- acmap(
titer_table = testtable
)
mode(testtable) <- "character"
expect_equal(
unname(titerTable(actablemap)),
testtable
)
ag_names <- paste("Antigen", 1:5)
sr_names <- paste("Serum", 1:5)
ag_coords <- matrix(1:10, 5, 2)
sr_coords <- matrix(11:20, 5, 2)
ag_coords3d <- cbind(ag_coords, 2)
sr_coords3d <- cbind(sr_coords, 2)
map <- acmap(
ag_names = ag_names,
sr_names = sr_names
)
expect_error(agCoords(map) <- ag_coords)
expect_error(srCoords(map) <- sr_coords)
map3d <- acmap(
ag_names = ag_names,
sr_names = sr_names
)
expect_error(agCoords(map) <- ag_coords3d, "optimization run not found")
expect_error(srCoords(map) <- sr_coords3d, "optimization run not found")
# expect_equal(unname(agCoords(map)), ag_coords)
# expect_equal(unname(srCoords(map)), sr_coords)
# expect_equal(unname(agCoords(map3d)), ag_coords3d)
# expect_equal(unname(srCoords(map3d)), sr_coords3d)
# expect_equal(numOptimizations(map), 1)
})
# Incorrect titers
test_that("Invalid titers", {
expect_equal(
numAntigens(acmap(
titer_table = matrix(c("*", "<20", "10", ">80"), 2, 2)
)),
2
)
check_titer_error <- function(titers) {
expect_error(
acmap(titer_table = matrix(titers, 2, 2))
)
}
check_titer_error(c("na", "<20", "10", ">80"))
check_titer_error(c("1'230", "<20", "10", ">80"))
check_titer_error(c("<>23", "<20", "10", ">80"))
check_titer_error(c("<=10", "<20", "10", ">80"))
check_titer_error(c("<10", "<20", "10", ">=80"))
})
# Incorrect arguments
test_that("Disallowed arguments", {
expect_error(make.acmap(ag_coords = matrix(1:10)))
expect_error(make.acmap(foo = "bar", bar = "foo"))
})
# Cloning
map <- read.acmap(filename = test_path("../testdata/testmap.ace"))
map2 <- keepSingleOptimization(map, 2)
test_that("Removing optimizations", {
expect_equal(numOptimizations(map), 3)
expect_equal(numOptimizations(map2), 1)
})
# Using acmap
test_that("Making a map and optimizing", {
map <- make.acmap(
titer_table = testtable,
number_of_dimensions = 3,
number_of_optimizations = 2,
minimum_column_basis = "none",
check_convergence = FALSE
)
expect_equal(numAntigens(map), 6)
expect_equal(numSera(map), 4)
})
test_that("Making a map and optimizing using table arg", {
expect_warning({
map <- make.acmap(
table = testtable,
number_of_dimensions = 3,
number_of_optimizations = 2,
minimum_column_basis = "none"
)
}, "Argument 'table' is deprecated, please use 'titer_table' instead")
expect_equal(numAntigens(map), 6)
expect_equal(numSera(map), 4)
})
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