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mini-pw · Oct 28, 2024 · 12014f3 · 12014f3
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commit 12014f3
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Showing 4 changed files with 19 additions and 12 deletions.
diff --git a/R/process-plate.R b/R/process-plate.R
@@ -75,8 +75,10 @@ is_valid_normalisation_type <- function(normalisation_type) {
 #' process_plate(plate, output_dir = example_dir)
 #'
 #' # process plate without adjusting blanks and save the output to a file with a custom name
-#' process_plate(plate, filename = "plate_without_blanks_adjusted.csv",
-#'    output_dir = example_dir, adjust_blanks = FALSE)
+#' process_plate(plate,
+#'   filename = "plate_without_blanks_adjusted.csv",
+#'   output_dir = example_dir, adjust_blanks = FALSE
+#' )
 #'
 #'
 #' # nMFI normalisation
@@ -105,8 +107,10 @@ process_plate <-
 
 
     output_path <- validate_filepath_and_output_dir(filename, output_dir,
-                                                    plate$plate_name, normalisation_type,
-                                                    "csv", verbose = verbose)
+      plate$plate_name, normalisation_type,
+      "csv",
+      verbose = verbose
+    )
 
 
     if (!plate$blank_adjusted && adjust_blanks) {

diff --git a/tests/testthat/test-generate_report.R b/tests/testthat/test-generate_report.R
@@ -33,7 +33,7 @@ test_that("Test generate_plate_report function", {
   expect_no_error(generate_plate_report(plate, output_dir = tmp_dir))
   expect_no_error(generate_plate_report(plate, output_dir = tmp_dir, filename = "test_report.html"))
   file.remove(file.path(tmp_dir, "test_report.html"))
-  expect_no_error(generate_plate_report(plate, output_dir = tmp_dir, filename = "test_report.html",  counts_lower_threshold = 40, counts_higher_threshold = 80))
+  expect_no_error(generate_plate_report(plate, output_dir = tmp_dir, filename = "test_report.html", counts_lower_threshold = 40, counts_higher_threshold = 80))
   file.remove(file.path(tmp_dir, "test_report.html"))
   expect_no_error(generate_plate_report(plate, output_dir = tmp_dir, filename = "test_report.html", additional_notes = "This is a test report."))
   file.remove(file.path(tmp_dir, "test_report.html"))
@@ -42,7 +42,6 @@ test_that("Test generate_plate_report function", {
   multiline_note <- "This is a test report.\nThis is a test report."
   expect_no_error(generate_plate_report(plate, output_dir = tmp_dir, filename = "test_report.html", additional_notes = multiline_note))
   file.remove(file.path(tmp_dir, "test_report.html"))
-
 })
 
 test_that("Test generate_levey_jennings_report function", {

diff --git a/tests/testthat/test-helpers.R b/tests/testthat/test-helpers.R
@@ -133,19 +133,23 @@ test_that("Test validate_filepath_and_output_dir function", {
 
   # filename with no output_dir
   expect_warning(
-    validate_filepath_and_output_dir(file.path(tmp_dir, "test.html"), tmp_dir, "plate_name", "report", "html"))
+    validate_filepath_and_output_dir(file.path(tmp_dir, "test.html"), tmp_dir, "plate_name", "report", "html")
+  )
 
   expect_no_warning(
-    validate_filepath_and_output_dir(file.path(tmp_dir, "test.html"), NULL, "plate_name", "report", "html"))
+    validate_filepath_and_output_dir(file.path(tmp_dir, "test.html"), NULL, "plate_name", "report", "html")
+  )
 
   file.create(file.path(tmp_dir, "test.html"))
   # overwrite existing file
   expect_warning(
-    validate_filepath_and_output_dir(file.path(tmp_dir, "test.html"), tmp_dir, "plate_name", "report", "html"))
+    validate_filepath_and_output_dir(file.path(tmp_dir, "test.html"), tmp_dir, "plate_name", "report", "html")
+  )
 
   # create output directory
   expect_no_error(
-    validate_filepath_and_output_dir("test.html", file.path(tmp_dir, "output"), "plate_name", "report", "html"))
+    validate_filepath_and_output_dir("test.html", file.path(tmp_dir, "output"), "plate_name", "report", "html")
+  )
 
   expect_true(dir.exists(file.path(tmp_dir, "output")))
 })
diff --git a/tests/testthat/test-process-plate.R b/tests/testthat/test-process-plate.R
@@ -46,7 +46,7 @@ test_that("Processing plate with nMFI", {
   file.remove(test_output_path)
   # Test processing of a plate with reference dilution specified
   expect_no_error(
-    process_plate(plate, output_dir = tmp_dir, filename = "output.csv",  normalisation_type = "nMFI", reference_dilution = "1/50")
+    process_plate(plate, output_dir = tmp_dir, filename = "output.csv", normalisation_type = "nMFI", reference_dilution = "1/50")
   )
   expect_true(file.exists(test_output_path))
   expect_no_error(dilutions <- read.csv(test_output_path))
@@ -85,7 +85,7 @@ test_that("raw MFI in dataframe", {
 
   # Test processing of a plate, with raw MFI
   expect_no_error(
-    output_df <- process_plate(plate, output_dir = tmp_dir, filename = "output.csv",  normalisation_type = "nMFI", include_raw_mfi = TRUE)
+    output_df <- process_plate(plate, output_dir = tmp_dir, filename = "output.csv", normalisation_type = "nMFI", include_raw_mfi = TRUE)
   )
   stopifnot(all(colnames(output_df) == c(plate$analyte_names, paste0(plate$analyte_names, "_raw"))))
 })