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mini-pw · Oct 16, 2024 · d3d2b5c · d3d2b5c
1 parent 722e98f
commit d3d2b5c
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Showing 6 changed files with 8 additions and 12 deletions.
diff --git a/R/generate_report.R b/R/generate_report.R
@@ -20,7 +20,7 @@
 #'
 #' plate <- read_luminex_data(plate_file, layout_file)
 #' tmp_dir <- tempdir(check = TRUE)
-#' generate_plate_report(plate, output_dir=tmp_dir, counts_lower_threshold = 40, counts_higher_threshold = 50)
+#' generate_plate_report(plate, output_dir = tmp_dir, counts_lower_threshold = 40, counts_higher_threshold = 50)
 #' @export
 generate_plate_report <- function(plate, use_model = TRUE, filename = NULL, output_dir = "reports", counts_lower_threshold = 50, counts_higher_threshold = 70) {
   message("Generating report... This will take approximately 30 seconds.")

diff --git a/R/helpers.R b/R/helpers.R
@@ -193,7 +193,7 @@ format_dilutions <- function(dilutions, dilution_values, sample_types) {
   paste(sorted_formatted_dilutions, collapse = ", ")
 }
 
-             
+
 #' Convert dilution to RAU
 #'
 #' @param predicted_dilution (`numeric()`) A numeric value representing the predicted dilution.

diff --git a/R/plots-standard_curve.R b/R/plots-standard_curve.R
@@ -120,7 +120,7 @@ plot_standard_curve_analyte <- function(plate,
     ) +
     ggplot2::guides(color = guide_legend(title = "Plot object"))
 
-  if(!plot_legend){
+  if (!plot_legend) {
     p <- p + ggplot2::theme(legend.position = "none")
   }
 
@@ -188,7 +188,7 @@ plot_standard_curve_analyte_with_model <- function(plate,
   test_samples_mfi <- plate$get_data(analyte_name, "TEST", data_type = data_type)
   test_sample_estimates <- predict(model, test_samples_mfi, ...)
 
-  
+
   if (plot_test_predictions) {
     p <- p + ggplot2::geom_point(
       ggplot2::aes(x = .data$RAU, y = .data$MFI, color = "Test sample predictions"),

diff --git a/tests/testthat/test-generate_report.R b/tests/testthat/test-generate_report.R
@@ -37,4 +37,4 @@ test_that("Test generate_levey_jennings_report function", {
   expect_error(generate_levey_jennings_report())
   expect_no_error(generate_levey_jennings_report(list(plate)))
   expect_no_error(generate_levey_jennings_report(list(plate), filename = "test_report.html"))
-})
+})
diff --git a/tests/testthat/test-helpers.R b/tests/testthat/test-helpers.R
@@ -50,7 +50,6 @@ test_that("Test clamp function", {
 })
 
 test_that("Test format dilution function standard case", {
-
   dilutions <- c("1/2", "1/3", "1/4")
   dilution_values <- c(0.5, 0.33, 0.25)
   sample_types <- c("STANDARD CURVE", "STANDARD CURVE", "STANDARD CURVE")
@@ -59,7 +58,6 @@ test_that("Test format dilution function standard case", {
 })
 
 test_that("Test format dilution function with sample types", {
-
   dilutions <- c("1/2", "1/3", "1/4")
   dilution_values <- c(0.5, 0.33, 0.25)
   sample_types <- c("STANDARD CURVE", "STANDARD CURVE", "SAMPLE")
@@ -68,7 +66,6 @@ test_that("Test format dilution function with sample types", {
 })
 
 test_that("Test format dilution function with multiple duplicates", {
-
   dilutions <- c("1/2", "1/3", "1/4", "1/4")
   dilution_values <- c(0.5, 0.33, 0.25, 0.25)
   sample_types <- c("STANDARD CURVE", "STANDARD CURVE", "STANDARD CURVE", "STANDARD CURVE")
@@ -77,7 +74,6 @@ test_that("Test format dilution function with multiple duplicates", {
 })
 
 test_that("Test format dilution function with shuffled dilutions", {
-
   dilutions <- c("1/4", "1/2", "1/3")
   dilution_values <- c(0.25, 0.5, 0.33)
   sample_types <- c("STANDARD CURVE", "STANDARD CURVE", "STANDARD CURVE")
@@ -86,7 +82,6 @@ test_that("Test format dilution function with shuffled dilutions", {
 })
 
 test_that("Test format dilution function with dilutions equal null", {
-
   dilutions <- NULL
   dilution_values <- c(0.25, 0.5, 0.33)
   sample_types <- c("STANDARD CURVE", "STANDARD CURVE", "SAMPLE")

diff --git a/tests/testthat/test-integration.R b/tests/testthat/test-integration.R
@@ -43,8 +43,9 @@ test_that("Fully Parse CovidOISExPONTENT_CO.csv plate data with layout", {
   test_output_path <- file.path(tmp_dir, "output.csv")
   expect_no_error(
     capture.output(
-                   process_plate(plate, output_path = test_output_path),
-                   file = NULL)
+      process_plate(plate, output_path = test_output_path),
+      file = NULL
+    )
   )
   expect_true(file.exists(test_output_path))
   expect_no_error(dilutions <- read.csv(test_output_path))