From 7889ed598130a2c0325e14cdf21e8b8d957280e7 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Tue, 23 Jul 2024 12:22:37 +0200
Subject: [PATCH] started refactoring

---
 DESCRIPTION                       |  2 +-
 R/adjust.time.R                   |  8 +++---
 tests/testthat/test-adjust-time.R | 42 +++++++++++++++++++++++++++++++
 3 files changed, 47 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 80196d4..3b1effc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,4 +17,4 @@ NeedsCompilation: no
 Suggests: 
     dataCompareR, testthat (>= 3.0.0), microbenchmark
 Config/testthat/edition: 3
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
diff --git a/R/adjust.time.R b/R/adjust.time.R
index 9a9a0bb..11d0a74 100644
--- a/R/adjust.time.R
+++ b/R/adjust.time.R
@@ -6,9 +6,8 @@ NULL
 compute_comb <- function(template_features, features) {
   combined <- dplyr::bind_rows(
     template_features,
-    dplyr::bind_cols(features |> dplyr::select(c(mz, rt, cluster)), sample_id = features$sample_id)
-  )
-  combined <- combined |> dplyr::arrange_at("mz")
+    features |> dplyr::select(c(mz, rt, cluster, sample_id))
+  ) |> dplyr::arrange_at(c("cluster","mz"))
   return(combined)
 }
 
@@ -38,6 +37,7 @@ compute_template_adjusted_rt <- function(combined, sel, j) {
 #' @export
 compute_corrected_features <- function(features, delta_rt, avg_time) {
   features <- features[order(features$rt, features$mz), ]
+
   corrected <- features$rt
   original <- features$rt
   to_correct <- original[original >= min(delta_rt) &
@@ -90,7 +90,7 @@ correct_time <- function(this.feature, template_features) {
     orig.features <- this.feature
     template <- unique(template_features$sample_id)[1]
     j <- unique(this.feature$sample_id)[1]
-    
+
     if (j != template) {
       this.comb <- compute_comb(template_features, this.feature)
       sel <- compute_sel(this.comb)
diff --git a/tests/testthat/test-adjust-time.R b/tests/testthat/test-adjust-time.R
index a57910f..fdd65ab 100644
--- a/tests/testthat/test-adjust-time.R
+++ b/tests/testthat/test-adjust-time.R
@@ -41,3 +41,45 @@ patrick::with_parameters_test_that(
     )
   )
 )
+
+test_that("compute_sel", {
+  testdata <- file.path("..", "testdata")
+  template_features <- file.path(testdata, "template", "RCX_shortened.parquet")
+  template_features <- arrow::read_parquet(template_features)
+
+  clustered_table <- read_parquet_files(
+    c("RCX_06_shortened"),
+    "clusters",
+    "_extracted_clusters.parquet"
+  )[[1]]
+
+  all_features <- compute_template_adjusted_rt(
+    compute_comb(template_features, clustered_table),
+    compute_sel(combined),
+    "RCX_07_shortened"
+  )
+
+  subsets <- template_features |>
+    dplyr::bind_rows(clustered_table |> dplyr::select(c(mz, rt, cluster, sample_id))) |>
+    dplyr::arrange_at(c("cluster","mz")) |>
+    dplyr::group_by(cluster) |>
+    mutate(count = n_distinct(sample_id)) |>
+    filter(count == 2) |>
+    add_count() |>
+    filter(n == 2) |>
+    ungroup() |>
+    group_by(sample_id) |>
+    group_split()
+
+  all_features_new <- cbind(subsets[[1]]$rt, subsets[[2]]$rt)
+  all_features_new_order <- order(all_features_new[,2])
+  all_features_new_arranged <- all_features_new[all_features_new_order,]
+
+  this.feature <- compute_corrected_features(
+    clustered_table,
+    all_features_new_arranged[, 2],
+    all_features_new_arranged[, 1] - all_features_new_arranged[, 2]
+  )
+
+  browser()
+})
\ No newline at end of file