feat: additional notes in report (#192)

* inital draft of notes

* implement additional notes in template

* implement in package code

* tests and multiline support

* improved docs and new test

* typos fix

* docs rerun

R/generate_report.R

@@ -10,6 +10,7 @@
 #' @param output_dir (`character(1)`) The directory where the report should be saved. Default is 'reports'.
 #' @param counts_lower_threshold (`numeric(1)`) The lower threshold for the counts plots (works for each analyte). Default is 50.
 #' @param counts_higher_threshold (`numeric(1)`) The higher threshold for the counts plots (works for each analyte). Default is 70.
+#' @param additional_notes (`character(1)`) Additional notes to be included in the report. Contents of this fields are left to the user's discretion. If not provided, the field will not be included in the report.
 #'
 #'
 #' @return A report.
@@ -18,28 +19,35 @@
 #'
 #' plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM")
 #' layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "PvSTATEM")
+#' note <- "This is a test report.\n**Author**: Jane Doe \n**Tester**: John Doe"
 #'
 #' 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
+#'   counts_lower_threshold = 40,
+#'   counts_higher_threshold = 50,
+#'   additional_notes = note
 #' )
 #' @export
-generate_plate_report <- function(plate, use_model = TRUE, filename = NULL, output_dir = "reports", counts_lower_threshold = 50, counts_higher_threshold = 70) {
+generate_plate_report <- function(plate, use_model = TRUE, filename = NULL, output_dir = "reports", counts_lower_threshold = 50, counts_higher_threshold = 70, additional_notes = NULL) {
   message("Generating report... This will take approximately 30 seconds.")
   output_file <- if (is.null(filename)) {
     paste0(plate$plate_name, "_report.html")
   } else {
     filename
   }
 
-
   template_path <- system.file("templates", "plate_report_template.Rmd", package = "PvSTATEM", mustWork = TRUE)
 
+  # markdown does not support single line breaks, so we need to replace them with two spaces and a line break
+  if (!is.null(additional_notes)) {
+    additional_notes <- gsub(pattern = "\n", replacement = "  \n", x = additional_notes)
+  }
+
   rmarkdown::render(
     template_path,
-    params = list(plate = plate, use_model = use_model, counts_lower_threshold = counts_lower_threshold, counts_higher_threshold = counts_higher_threshold),
+    params = list(plate = plate, use_model = use_model, counts_lower_threshold = counts_lower_threshold, counts_higher_threshold = counts_higher_threshold, additional_notes = additional_notes),
     output_file = output_file,
     output_dir = output_dir,
     quiet = TRUE

R/get-nmfi.R

@@ -41,7 +41,7 @@
 #' # calculate the nMFI values
 #' nmfi <- get_nmfi(plate, reference_dilution = 1 / 400)
 #'
-#' # we don't do any extrapolation and the values should be comparable accross plates
+#' # we don't do any extrapolation and the values should be comparable across plates
 #' head(nmfi)
 #' # different params
 #' nmfi <- get_nmfi(plate, reference_dilution = "1/50")

inst/templates/levey_jennings_report_template.Rmd

@@ -4,6 +4,8 @@ output: html_document
 params:
   list_of_plates: !r NULL
 ---
+Report generated on:  `r format(Sys.time(), "%d-%m-%Y %H:%M:%S")`.  
+------------------
 
 ###  
 

inst/templates/plate_report_template.Rmd

@@ -6,6 +6,7 @@ params:
   use_model: !r NULL
   counts_lower_threshold: !r NULL
   counts_higher_threshold: !r NULL
+  additional_notes: !r NULL
 ---
 
 ```{r param-check, echo=FALSE}
@@ -33,6 +34,9 @@ if (!is(params$counts_lower_threshold, "numeric")) {
 if (!is(params$counts_higher_threshold, "numeric")) {
   stop("The `counts_higher_threshold` must be a numeric value.")
 }
+if (!is.null(params$additional_notes) && !is(params$additional_notes, "character")) {
+  stop("The `additional_notes` must be a character value.")
+}
 ```
 
 Report generated on:  `r format(Sys.time(), "%d-%m-%Y %H:%M:%S")`.  
@@ -41,8 +45,13 @@ Plate batch name: `r if(!is.null(params$plate$batch_name)) params$plate$batch_na
 This is plate with `r paste0(length(params$plate$sample_names), " samples and ", length(params$plate$analyte_names), " analytes")`.  
 Standard curve sample dilutions: `r format_dilutions(params$plate$dilutions, params$plate$dilution_values, params$plate$sample_types)`.
 
+------------------
+
+`r if(!is.null(params$additional_notes)) "### Additional notes \n" `  
+
+`r if(!is.null(params$additional_notes)) params$additional_notes `  
 
--------------------
+`r if(!is.null(params$additional_notes)) "\n -------------------" ` 
 
 
 ### Plate layout
@@ -177,7 +186,7 @@ cat('</div>')
 
 ------------------
 
-### Details for given analayte {.tabset .tabset-fade}
+### Details for given analyte {.tabset .tabset-fade}
 
 ```{r quality-control, results='asis', echo=FALSE, message=FALSE, out.width="50%", dev='jpeg', dpi=72}
 # Code used to create dynamic tabs based on the number of analytes

tests/testthat/test-generate_report.R

@@ -30,6 +30,10 @@ test_that("Test generate_plate_report function", {
   expect_no_error(generate_plate_report(plate))
   expect_no_error(generate_plate_report(plate, filename = "test_report.html"))
   expect_no_error(generate_plate_report(plate, counts_lower_threshold = 40, counts_higher_threshold = 80))
+  expect_no_error(generate_plate_report(plate, additional_notes = "This is a test report."))
+
+  multiline_note <- "This is a test report.\nThis is a test report."
+  expect_no_error(generate_plate_report(plate, additional_notes = multiline_note))
 })
 
 test_that("Test generate_levey_jennings_report function", {