context("Dimensionality reduction")
test_that("With generated data", {
dataset <- generate_dataset(num_genes = 500, num_samples = 300, num_groups = 4)
expression <- dataset$expression
# testing for 1 dimension
space <- reduce_dimensionality(expression, "spearman", ndim = 1)
traj <- infer_trajectory(space)
expect_is(traj, "list")
expect_is(traj, "SCORPIUS::trajectory")
expect_equal(names(traj), c("path", "time"))
expect_equal( ncol(traj$path), ncol(space) )
expect_equal( colnames(traj$path), colnames(space) )
expect_equal( length(traj$time), nrow(expression) )
expect_equal( names(traj$time), rownames(expression) )
# testing for 2 dimensions
space <- reduce_dimensionality(expression, "spearman", ndim=2)
traj <- infer_trajectory(space)
expect_is(traj, "list")
expect_is(traj, "SCORPIUS::trajectory")
expect_equal(names(traj), c("path", "time"))
expect_equal( ncol(traj$path), ncol(space) )
expect_equal( colnames(traj$path), colnames(space) )
expect_equal( length(traj$time), nrow(expression) )
expect_equal( names(traj$time), rownames(expression) )
# reverse_trajectory
rev_traj <- reverse_trajectory(traj)
expect_is(rev_traj, "list")
expect_is(rev_traj, "SCORPIUS::trajectory")
expect_equal(names(rev_traj), c("path", "time"))
expect_equal( ncol(rev_traj$path), ncol(space) )
expect_equal( colnames(rev_traj$path), colnames(space) )
expect_equal( length(rev_traj$time), nrow(expression) )
expect_equal( names(rev_traj$time), rownames(expression) )
})
test_that("With generated data and edge case", {
dataset <- generate_dataset(num_genes = 500, num_samples = 10, num_groups = 4)
expression <- dataset$expression
# testing for 1 dimension
space <- reduce_dimensionality(expression, "spearman", ndim=1)
traj <- infer_trajectory(space)
expect_is(traj, "list")
expect_is(traj, "SCORPIUS::trajectory")
expect_equal(names(traj), c("path", "time"))
expect_equal( ncol(traj$path), ncol(space) )
expect_equal( colnames(traj$path), colnames(space) )
expect_equal( length(traj$time), nrow(expression) )
expect_equal( names(traj$time), rownames(expression) )
# testing for 2 dimensions
space <- reduce_dimensionality(expression, "spearman", ndim = 2)
traj <- infer_trajectory(space)
expect_is(traj, "list")
expect_is(traj, "SCORPIUS::trajectory")
expect_equal(names(traj), c("path", "time"))
expect_equal( ncol(traj$path), ncol(space) )
expect_equal( colnames(traj$path), colnames(space) )
expect_equal( length(traj$time), nrow(expression) )
expect_equal( names(traj$time), rownames(expression) )
# reverse_trajectory
rev_traj <- reverse_trajectory(traj)
expect_is(rev_traj, "list")
expect_is(rev_traj, "SCORPIUS::trajectory")
expect_equal(names(rev_traj), c("path", "time"))
expect_equal( ncol(rev_traj$path), ncol(space) )
expect_equal( colnames(rev_traj$path), colnames(space) )
expect_equal( length(rev_traj$time), nrow(expression) )
expect_equal( names(rev_traj$time), rownames(expression) )
})
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