more tests

R/mutates.R

@@ -150,6 +150,9 @@ center <- function(x) {
 #'   mutate(new_sample_var = "foo") %>%
 #'   select(-DR)
 #' new_variable_tables <- c("new_sample_var" = "samples")
+#'
+#' update_tidy_omic(tidy_omic, updated_tidy_data, new_variable_tables)
+#'
 #' @export
 update_tidy_omic <- function(
     tidy_omic,

tests/testthat/_snaps/design.md

@@ -17,3 +17,19 @@
        9 sample          sample_primary_key  measurements
       10 expression      numeric             measurements
 
+# Catch malformed design objects
+
+    Code
+      check_design(malformed_design)
+    Condition
+      Error in `check_design()`:
+      ! The following unexpected attributes were found in the design: foo
+
+---
+
+    Code
+      check_design(malformed_design)
+    Condition
+      Error in `check_design()`:
+      ! The following attributes were missing in the design: feature_pk
+

tests/testthat/_snaps/dim_reduction.md

@@ -0,0 +1,20 @@
+# Sample mahalanobis distances are calculated
+
+    Code
+      pc_distances
+    Output
+      # A tibble: 36 x 4
+         sample nutrient    DR pc_distance
+         <chr>  <chr>    <dbl>       <dbl>
+       1 G0.05  G         0.05       188. 
+       2 G0.1   G         0.1        125. 
+       3 G0.15  G         0.15       128. 
+       4 G0.2   G         0.2        125. 
+       5 G0.25  G         0.25        83.4
+       6 G0.3   G         0.3        101. 
+       7 N0.05  N         0.05       371. 
+       8 N0.1   N         0.1        226. 
+       9 N0.15  N         0.15       123. 
+      10 N0.2   N         0.2        100. 
+      # i 26 more rows
+

tests/testthat/_snaps/mutates.md

@@ -36,3 +36,55 @@
       ! bar is not present in measurements, valid value_vars include:
       expression
 
+# Factor levels can be updated using a list of factor orders
+
+    Code
+      brauer_w_mystery_nutrients <- update_sample_factors(brauer_2008_tidy_w_NAs,
+        list(nutrient = NUTRIENT_ORDER))
+    Message
+      ! NA was present in the sample metadata's nutrient field but did not have a corresponding factor level in the `factor_levels` list. They will be added to the end of the specified factor levels
+      ! The nutrient field in the sample metadata contains 2 NA values. These entries will be replaced with an "unspecified" level.
+
+---
+
+    Code
+      reordered_tidy <- update_sample_factors(brauer_2008_tidy, list(nutrient = CONFUSED_NUTRIENT_ORDER))
+    Message
+      ! "G" was present in the sample metadata's nutrient field but did not have a corresponding factor level in the `factor_levels` list. They will be added to the end of the specified factor levels
+      ! "C" was present in `factor_levels` for nutrient but did not have a corresponding entry in the sample metadata.
+
+---
+
+    Code
+      update_sample_factors(brauer_2008_tidy, list(nutrient = 1:5))
+    Condition
+      Error in `set_factor_levels()`:
+      ! The factor levels for nutrient were "integer". This should be a character vector.
+
+---
+
+    Code
+      update_sample_factors(brauer_2008_tidy, list(nutrient = c("G", "G", "N", "L")))
+    Condition
+      Error in `set_factor_levels()`:
+      ! 1 factor levels was duplicated in the `factor_levels` specification for "nutrient": G
+
+---
+
+    Code
+      update_sample_factors(brauer_2008_tidy, list(DR = seq(0.05, 0.3, by = 0.05)))
+    Condition
+      Error in `set_factor_levels()`:
+      ! The factor levels for DR were "numeric". This should be a character vector.
+
+# Update tidy omics with new added variables
+
+    Code
+      update_tidy_omic(tidy_omic, updated_tidy_data, c())
+    Condition
+      Error in `update_tidy_omic()`:
+      ! updated_tidy_data contains 1
+      - new fields: new_sample_var.
+      - Add these to "new_variable_tables" so that romic know how to
+      - use them.
+

tests/testthat/test-design.R

@@ -5,3 +5,31 @@ test_that("extract design as a table", {
   expect_invisible(check_design_in_tomic(brauer_2008_tidy))
 })
 
+test_that("get_design_tbl() works when directly passing a design instead of a tomic", {
+  expect_equal(
+    get_design_tbl(brauer_2008_tidy),
+    get_design_tbl(brauer_2008_tidy$design)
+  )
+})
+
+test_that("Catch malformed design objects", {
+
+  malformed_design <- brauer_2008_tidy$design
+  malformed_design$foo <- "bar"
+
+  expect_snapshot(
+    check_design(malformed_design),
+    error = TRUE
+  )
+
+
+  malformed_design <- brauer_2008_tidy$design
+  malformed_design$feature_pk <- NULL
+
+  expect_snapshot(
+    check_design(malformed_design),
+    error = TRUE
+  )
+
+})
+

tests/testthat/test-dim_reduction.R

@@ -41,3 +41,10 @@ test_that("Matrices keys are reconstructed with appropriate classes", {
   }
 
 })
+
+test_that("Sample mahalanobis distances are calculated", {
+
+  pc_distances <- calculate_sample_mahalanobis_distances(brauer_2008_tidy)
+  expect_snapshot(pc_distances)
+
+})

tests/testthat/test-mutates.R

@@ -75,3 +75,87 @@ test_that("Sort tomic applies a sort to features and/or samples", {
     expect_equal("fully sorted")
 })
 
+test_that("Factor levels can be updated using a list of factor orders", {
+
+  NUTRIENT_ORDER <- c("G", "N", "P", "S", "L", "U")
+
+  reordered_tidy <- update_sample_factors(
+    brauer_2008_tidy,
+    list(nutrient = NUTRIENT_ORDER)
+    )
+
+  expect_equal(levels(reordered_tidy$data$nutrient), NUTRIENT_ORDER)
+
+  # test NA handling
+  brauer_samples <- get_tomic_table(brauer_2008_tidy, "samples")
+  brauer_samples$nutrient[1:2] <- NA
+
+  brauer_2008_tidy_w_NAs <- update_tomic(
+    brauer_2008_tidy,
+    brauer_samples
+  )
+
+  expect_snapshot(
+    brauer_w_mystery_nutrients <- update_sample_factors(
+      brauer_2008_tidy_w_NAs,
+      list(nutrient = NUTRIENT_ORDER)
+    )
+  )
+
+  expect_equal(
+    levels(brauer_w_mystery_nutrients$data$nutrient),
+    c(NUTRIENT_ORDER, "unspecified")
+  )
+
+  # W/ unexpected levels
+
+  CONFUSED_NUTRIENT_ORDER <- c("C", "N", "P", "S", "L", "U")
+
+  expect_snapshot(
+    reordered_tidy <- update_sample_factors(
+      brauer_2008_tidy,
+      list(nutrient = CONFUSED_NUTRIENT_ORDER)
+    ))
+
+  expect_equal(levels(reordered_tidy$data$nutrient), c(CONFUSED_NUTRIENT_ORDER, "G"))
+
+  # invalid factor specifications
+
+  expect_snapshot(
+    update_sample_factors(brauer_2008_tidy, list(nutrient = 1:5)),
+    error = TRUE
+  )
+
+  expect_snapshot(
+    update_sample_factors(brauer_2008_tidy, list(nutrient = c("G", "G", "N", "L"))),
+    error = TRUE
+  )
+
+  expect_snapshot(
+    update_sample_factors(brauer_2008_tidy, list(DR = seq(0.05, 0.3, by = 0.05))),
+    error = TRUE
+  )
+
+})
+
+test_that("Update tidy omics with new added variables", {
+
+  tidy_omic <- brauer_2008_tidy
+  updated_tidy_data <- tidy_omic$data %>%
+    dplyr::mutate(new_sample_var = "foo") %>%
+    dplyr::select(-DR)
+
+  new_variable_tables <- c("new_sample_var" = "samples")
+
+  tidy_w_updated_samples <- update_tidy_omic(tidy_omic, updated_tidy_data, new_variable_tables)
+  expect_equal(
+    tidy_w_updated_samples$design$samples$variable,
+    c('sample', "nutrient", "new_sample_var")
+  )
+
+  expect_snapshot(
+    update_tidy_omic(tidy_omic, updated_tidy_data, c()),
+    error = TRUE
+    )
+
+})