Merge branch 'master' into SNplot_changes

RECETOX · Oct 30, 2024 · 792b88f · 792b88f
2 parents 40512d6 + e73eb0a
commit 792b88f
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Showing 27 changed files with 32 additions and 12 deletions.
diff --git a/R/IsoFiltR.R b/R/IsoFiltR.R
@@ -47,7 +47,7 @@ create_data_chunks <- function(data1) {
 
   data_chunks <- list()
   for (i in 1:10) {
-    start_idx <- (i - 1) * sect + 1
+    start_idx <- max((i-1)*sect, 1)
     end_idx <- min((i * sect + over), nrow(data1))
     data_chunks[[i]] <- data1[start_idx:end_idx, ]
   }
@@ -204,6 +204,14 @@ IsoFiltR <- function(
   IsoOutC2_final <- unique(IsoOutC2_final)
   MonoOutC_final <- unique(MonoOutC_final)
 
+  dummy <- data.frame(Exp_mass = -42, Abundance = -42, RT = -42)
+
+  IsoOutC1_final <- rbind(IsoOutC1_final, dummy)
+  IsoOutC2_final <- rbind(IsoOutC2_final, dummy)
+  MonoOutC_final <- rbind(MonoOutC_final, dummy)
+  MonoOutS_final <- rbind(MonoOutS_final, dummy)
+  IsoOutS_final <- rbind(IsoOutS_final, dummy)
+
   IsoOutC1_final$Tag <- "C13"
   IsoOutC2_final$Tag <- "2C13"
   MonoOutC_final$Tag <- "C"
@@ -465,7 +473,7 @@ process_sulfur <- function(raw_data, sulferr, data_end, sulfrat) {
     normalization_factor = 12,
     multiplier = 2,
     pair_thresold = c(-1.990, -2),
-    filter_criteria = c(0.00149, -0.29051, -0.29349, 0.70949, 0.7075)
+    filter_criteria = c(0.00249, -0.29051, -0.29349, 0.70949, 0.7075)
   )
 
   data_end2 <- data_end

diff --git a/changelog.txt b/changelog.txt
@@ -1,5 +1,8 @@
 Package Updates
 
+10/30/2024 Version 1.1.2
+ - aligned IsoFiltR function with upstream version [#70](https://github.com/RECETOX/MFAssignR/pull/70)
+
 09/12/2024 Version 1.1.1
  - quick fix of hardcoded paths and imports [#59](https://github.com/RECETOX/MFAssignR/pull/59)
 

diff --git a/tests/testthat/test-IsoFiltR.R b/tests/testthat/test-IsoFiltR.R
@@ -1,8 +1,14 @@
+update_expected <- function(actual, expected_path) {
+  saveRDS(actual, file = expected_path)
+}
+
 patrick::with_parameters_test_that("IsoFiltR works",
   {
     raw <- read.csv(file.path("test-data", paste0("QC1_1_", toupper(mode), "_500.csv")))
     actual <- IsoFiltR(raw)
-    expected <- readRDS(file.path("test-data", paste0(mode, "_iso.rds")))
+    expected_path <- file.path("test-data", paste0(mode, "_iso.rds"))
+    expected <- readRDS(expected_path)
+
     expect_equal(actual, expected)
   },
   mode = c("pos", "neg")
@@ -20,7 +26,6 @@ test_that("IsoFiltR works on recetox-aplcms output", {
 
 patrick::with_parameters_test_that("filtered_data_is_empty works", {
   expect_equal(filtered_data_is_empty(test_data), expected)
-
   },
   patrick::cases(
     empty = list(test_data=list(content=c()), expected=TRUE),

diff --git a/tests/testthat/test-MFAssign.R b/tests/testthat/test-MFAssign.R
@@ -15,7 +15,7 @@ load_expected <- function(mode) {
   ))
 }
 
-save_expected <- function(actual, mode) {
+update_expected <- function(actual, mode) {
   paths <- expected_paths(mode)
   saveRDS(actual$Unambig, paths$unambig)
   saveRDS(actual$Ambig, paths$ambig)

diff --git a/tests/testthat/test-RecalFunctions.R b/tests/testthat/test-RecalFunctions.R
@@ -46,23 +46,24 @@ patrick::with_parameters_test_that("RecalList works",
     unambig <- readRDS(file.path("test-data", paste0(mode, "_cho_unambig.rds")))
 
     actual <- MFAssignR::RecalList(unambig)
+
     expected <- readRDS(expected_path)
 
     actual <- actual %>% dplyr::select(-"Series.Index")
     expected <- expected %>% dplyr::select(-"Series.Index")
     actual_sorted <- dplyr::arrange_at(actual, "Series")
     expected_sorted <- dplyr::arrange_at(expected, "Series")
-    
+
     expect_equal(actual_sorted, expected_sorted)
   },
   mode = c("neg", "pos"),
 )
 
 test_that("Replicate the Recal bug", {
-  unambig <- read.delim("test-data/bug_unambig.tabular")
-  mono <- read.delim("test-data/bug_mono.tabular")
-  iso <- read.delim("test-data/bug_iso.tabular")
-  recallist <- read.delim("test-data/bug_recalseries.tabular")
+  unambig <- read.delim(file.path("test-data", "bug_unambig.tabular"))
+  mono <- read.delim(file.path("test-data", "bug_mono.tabular"))
+  iso <- read.delim(file.path("test-data", "bug_iso.tabular"))
+  recallist <- read.delim(file.path("test-data", "bug_recalseries.tabular"))
 
   actual <- MFAssignR::Recal(
       df = unambig,
@@ -80,7 +81,8 @@ test_that("Replicate the Recal bug", {
       mzRange = 50,
       CalPeak = 150
     )
-    expected <- readRDS("test-data/bug_recal_expected.rds")
+    expected_path <- file.path("test-data", "bug_recal_expected.rds")
+    expected <- readRDS(expected_path)
     expect_equal(actual, expected)
 })
 
@@ -102,7 +104,9 @@ patrick::with_parameters_test_that("Replicate Recal isopeaks error", {
       series5 = recallist$Series[5],
       mzRange = 80
     )
-    expected <- readRDS("test-data/recal_isopeaks.rds")
+    expected_path <- file.path("test-data", "recal_isopeaks.rds")
+
+    expected <- readRDS(expected_path)
 
     expect_equal(actual, expected)
 },

diff --git a/tests/testthat/test-data/21_qc_no_dil_milliq_iso.rds b/tests/testthat/test-data/21_qc_no_dil_milliq_iso.rds
diff --git a/tests/testthat/test-data/bug_recal_expected.rds b/tests/testthat/test-data/bug_recal_expected.rds
diff --git a/tests/testthat/test-data/neg_ambig.rds b/tests/testthat/test-data/neg_ambig.rds
diff --git a/tests/testthat/test-data/neg_cho_ambig.rds b/tests/testthat/test-data/neg_cho_ambig.rds
diff --git a/tests/testthat/test-data/neg_cho_none.rds b/tests/testthat/test-data/neg_cho_none.rds
diff --git a/tests/testthat/test-data/neg_cho_unambig.rds b/tests/testthat/test-data/neg_cho_unambig.rds
diff --git a/tests/testthat/test-data/neg_iso.rds b/tests/testthat/test-data/neg_iso.rds
diff --git a/tests/testthat/test-data/neg_none.rds b/tests/testthat/test-data/neg_none.rds
diff --git a/tests/testthat/test-data/neg_recal_iso.rds b/tests/testthat/test-data/neg_recal_iso.rds
diff --git a/tests/testthat/test-data/neg_recal_mono.rds b/tests/testthat/test-data/neg_recal_mono.rds
diff --git a/tests/testthat/test-data/neg_recallist.rds b/tests/testthat/test-data/neg_recallist.rds
diff --git a/tests/testthat/test-data/neg_unambig.rds b/tests/testthat/test-data/neg_unambig.rds
diff --git a/tests/testthat/test-data/pos_ambig.rds b/tests/testthat/test-data/pos_ambig.rds
diff --git a/tests/testthat/test-data/pos_cho_ambig.rds b/tests/testthat/test-data/pos_cho_ambig.rds
diff --git a/tests/testthat/test-data/pos_cho_none.rds b/tests/testthat/test-data/pos_cho_none.rds
diff --git a/tests/testthat/test-data/pos_cho_unambig.rds b/tests/testthat/test-data/pos_cho_unambig.rds
diff --git a/tests/testthat/test-data/pos_iso.rds b/tests/testthat/test-data/pos_iso.rds
diff --git a/tests/testthat/test-data/pos_none.rds b/tests/testthat/test-data/pos_none.rds
diff --git a/tests/testthat/test-data/pos_recal_iso.rds b/tests/testthat/test-data/pos_recal_iso.rds
diff --git a/tests/testthat/test-data/pos_recal_mono.rds b/tests/testthat/test-data/pos_recal_mono.rds
diff --git a/tests/testthat/test-data/pos_unambig.rds b/tests/testthat/test-data/pos_unambig.rds
diff --git a/tests/testthat/test-data/recal_isopeaks.rds b/tests/testthat/test-data/recal_isopeaks.rds