Use z-score scaling_method and updated expected stretch and shift val…

…ues in registration unit tests

tests/testthat/test-dynamics.R

@@ -4,7 +4,7 @@ query <- "Col0"
 gene_data <- brapa_sample_data[gene_id == "BRAA03G051930.3C"]
 
 test_that("calc_loglik_H1 and calc_loglik_H2 work", {
-  all_data <- preprocess_data(gene_data, reference, query)
+  all_data <- preprocess_data(gene_data, reference, query, scaling_method = "z-score")
 
   # Expected outputs
   expect_no_error(calc_loglik_H2(all_data))

tests/testthat/test-optimisation.R

@@ -2,7 +2,7 @@ brapa_sample_data <- data.table::fread(system.file("extdata/brapa_arabidopsis_al
 reference <- "Ro18"
 query <- "Col0"
 gene_data <- brapa_sample_data[gene_id == "BRAA03G051930.3C"]
-all_data <- preprocess_data(gene_data, reference, query)
+all_data <- preprocess_data(gene_data, reference, query, scaling_method = "z-score")
 
 test_that("get_search_space_limits works", {
   space_lims <- get_search_space_limits(all_data)
@@ -35,7 +35,7 @@ test_that("get_search_space_limits_from_params works", {
 })
 
 test_that("calc_overlapping_percent works", {
-  all_data_reg <- apply_registration(all_data, 2.75, 3.6)
+  all_data_reg <- apply_registration(all_data, 3.10, 2.13)
   overlapping_raw <- calc_overlapping_percent(all_data)
   overlapping_reg <- calc_overlapping_percent(all_data_reg)
 
@@ -46,7 +46,7 @@ test_that("calc_overlapping_percent works", {
 
 test_that("objective_fun works", {
   # Expected outputs
-  expect_equal(objective_fun(all_data, 2.75, 3.6, 0.5), -11.19, tolerance = 1e-2)
+  expect_equal(objective_fun(all_data, 3.10, 2.13, 0.5), -11.19, tolerance = 1e-2)
   expect_equal(objective_fun(all_data), -999)
 })
 

tests/testthat/test-registration.R

@@ -8,20 +8,22 @@ gene_data <- brapa_sample_data[gene_id == "BRAA03G051930.3C"]
 test_that("preprocess_data works", {
   all_data <- preprocess_data(brapa_sample_data, reference, query)
   all_data_norm <- preprocess_data(brapa_sample_data, reference, query, scaling_method = "z-score")
+  all_data_minmax <- preprocess_data(brapa_sample_data, reference, query, scaling_method = "min-max")
 
   # Expected outputs
   expect_equal(class(all_data)[1], "data.table")
   expect_equal(class(all_data_norm)[1], "data.table")
+  expect_equal(class(all_data_minmax)[1], "data.table")
   expect_gte(mean(all_data$expression_value), mean(all_data_norm$expression_value))
   expect_equal(colnames(all_data), c(colnames(brapa_sample_data), "time_delta", "var"))
   expect_equal(levels(unique(all_data$accession)), c("ref", "query"))
   expect_equal(nrow(all_data), nrow(brapa_sample_data))
 })
 
 test_that("register_manually works", {
-  gene_data <- preprocess_data(gene_data, reference, query)
-  stretch <- 2.75
-  shift <- 3.6
+  gene_data <- preprocess_data(gene_data, reference, query, scaling_method = "z-score")
+  stretch <- 3.10
+  shift <- 2.13
   loglik_separate <- -10.404
   results <- register_manually(gene_data, stretch, shift, loglik_separate)
   results_simple <- register_manually(gene_data, stretch, shift, loglik_separate, return_data_reg = FALSE)
@@ -40,15 +42,16 @@ test_that("register_manually works", {
 # Full pipeline ----
 
 test_that("register (with no optimisation) works", {
-  stretch <- 2.75
-  shift <- 3.6
+  stretch <- 3.10
+  shift <- 2.13
   registration_results <- register(
     gene_data,
     reference = "Ro18",
     query = "Col0",
     stretches = stretch,
     shifts = shift,
-    optimise_registration_parameters = FALSE
+    optimise_registration_parameters = FALSE,
+    scaling_method = "z-score"
   ) |>
     suppressMessages()
 
@@ -68,7 +71,8 @@ test_that("register (with optimisation) works", {
     gene_data,
     reference = "Ro18",
     query = "Col0",
-    optimisation_method = "nm",
+    optimisation_method = "lbfgsb",
+    scaling_method = "z-score",
     optimisation_config = list(num_iterations = 10, num_fun_evals = 10)
   ) |>
     suppressMessages()
@@ -81,7 +85,7 @@ test_that("register (with optimisation) works", {
   expect_equal(colnames(data_reg), c("gene_id", "accession", "expression_value", "replicate", "timepoint", "timepoint_reg"))
   expect_equal(colnames(model_comparison), c("gene_id", "stretch", "shift", "BIC_diff", "registered"))
   expect_equal(model_comparison$registered, TRUE)
-  expect_equal(model_comparison$stretch, 2.809, tolerance = 1e-2)
-  expect_equal(model_comparison$shift, 0.143, tolerance = 1e-2)
+  expect_equal(model_comparison$stretch, 3.10, tolerance = 1e-2)
+  expect_equal(model_comparison$shift, 2.13, tolerance = 1e-2)
   expect_error(register(gene_data, reference = "Ro19", query = "Col0"))
 })