implemented passing unstructured data during tomic_to coercion

R/data_classes.R

@@ -638,6 +638,11 @@ triple_to_tidy <- function(triple_omic) {
   output$data <- tidy_output
   output$design <- triple_omic$design
 
+  if ("unstructured" %in% names(triple_omic)) {
+    # copy unstructured data as-is
+    output$unstructured <- triple_omic$unstructured
+  }
+
   class(output) <- c("tidy_omic", "tomic", class(triple_omic)[3])
 
   output
@@ -691,6 +696,11 @@ tidy_to_triple <- function(tidy_omic) {
     design = tidy_omic$design
   )
 
+  if ("unstructured" %in% names(tidy_omic)) {
+    # copy unstructured data as-is
+    output$unstructured <- tidy_omic$unstructured
+  }
+
   class(output) <- c("triple_omic", "tomic", class(tidy_omic)[3])
 
   output

R/dim_reduction.R

@@ -251,7 +251,9 @@ impute_missing_values <- function(
     tomic,
     impute_var_name = "imputed",
     value_var = NULL,
-    ...) {
+    ...
+    ){
+
   if (!("impute" %in% rownames(utils::installed.packages()))) {
     stop("Install \"impute\" using remotes::install_bioc(\"impute\") to use this function")
   }

tests/testthat/test-data_classes.R

@@ -111,6 +111,19 @@ test_that("Create triple omic", {
     sample_pk = "sample_id"
   )
 
+  testthat::expect_s3_class(simple_triple, "triple_omic")
+})
+
+test_that("Unstructured data preserved using tomic_to", {
+
+  triple_omic <- tomic_to(simple_triple, "triple_omic")
+  triple_omic$unstructured$dat <- "test"
+
+  tidy_copy <- triple_to_tidy(triple_omic)
+  expect_equal(tidy_copy$unstructured$dat, "test")
+
+  triple_restore <- tidy_to_triple(tidy_copy)
+  expect_equal(triple_restore$unstructured$dat, "test")
 })