context("test similarity")
test_that("euclid distance works",{
x_same <- euclid_dist(c(1,2), c(1,2))
x_dist <- euclid_dist(c(1,1), c(2,2))
expect_equal(x_same, 0)
})
test_that("expand_grid_unique works",{
a <- c(1,2,3)
b <- c('a', 'b', 'c')
out <- expand_grid_unique(a, b)
out_false <- expand_grid_unique(a, a, include.equals = TRUE)
expect_equal(dim(out), c(9, 2))
expect_equal(
dim(expand_grid_unique(c(1,2,3), c(1,2,3), include.equals = TRUE)),
c(6,2))
expect_equal(
dim(expand_grid_unique(c(1,2,3), c(1,2,3), include.equals = FALSE)),
c(3,2))
})
data(ex_data)
metadata <- construct_metadata(ex_data,
compound_col = 'Metadata_compound',
conc_col = 'Metadata_concentration',
feature_cols = 2:68,
negative_control = "DMSO")
compound_data <- get_compound_data(ex_data, metadata)
negative_control <- get_negative_control(ex_data, metadata)
d_out <- calculate_d(compound_data, negative_control)
d_scale <- scale_d(d_out)
out <- correlate(d_scale, metadata)
out_full <- correlate(d_scale, metadata, return_max = FALSE)
ans <- trim(d_scale, out, metadata = metadata)
sim_list <- similarity_list(ans)
test_that("similarity_list works",{
expect_true(class(sim_list) == 'dist')
diag_out <- as.numeric(diag(as.matrix(sim_list)))
expect_equal(diag_out, rep(0, 10))
})
test_that("similarity_df works",{
sim_df <- similarity_df(d_scale)
expect_true(class(sim_df) == 'dist')
})
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