Levey-Jennings Raport: `r paste0('*', params$report_title, '*')`

In SerolyzeR: Reading, Quality Control and Preprocessing of MBA (Multiplex Bead Assay) Data

list_of_plates <- params$list_of_plates
additional_notes <- params$additional_notes

if (is.null(list_of_plates)) {
  stop("The `list_of_plates` must be provided when rendering the document.")
}
if (!is.list(list_of_plates)) {
  stop("The `list_of_plates` must be a list of `Plate` instances.")
}
if (length(list_of_plates) == 0) {
  stop("The `list_of_plates` must contain at least one `Plate` instance.")
}
if (length(list_of_plates) < 10) {
  warning("The `list_of_plates` should contain at least 10 `Plate` instances to generate a comprehensive report.")
}
if (!all(sapply(list_of_plates, inherits, "Plate"))) {
  stop("The list_of_plates contains objects that are not of class Plate.")
}
if (is.null(params$report_title)) {
  stop("The `report_title` must be provided when rendering the document.")
}
if (!is(params$report_title, "character")) {
  stop("The `report_title` must be a character value.")
}
if (is.null(params$dilutions)) {
  stop("The `dilutions` must be provided when rendering the document.")
}
if (!is.character(params$dilutions)) {
  stop("The `dilutions` must be a character value.")
}
if (!all(grepl("(^1\\s*)\\/(\\s*\\d+$)", params$dilutions))) {
  stop("The `dilutions` must be in the format '1/digit'.")
}
for (dilution in params$dilutions) {
  if (!all(sapply(list_of_plates, function(plate) dilution %in% plate$get_dilution("STANDARD CURVE")))) {
    plate_where_dilution_is_missing <- which(sapply(list_of_plates, function(plate) !(dilution %in% plate$get_dilution("STANDARD CURVE"))))
    stop("The dilution",
         dilution,
         "is not present in plates ",
         paste(plate_where_dilution_is_missing, collapse = ", "))
  }
}
all_analyte_names <- c()

intersection_analytes <- list_of_plates[[1]]$analyte_names

for (plate in list_of_plates) {
  all_analyte_names <- union(all_analyte_names, plate$analyte_names)
  intersection_analytes <- intersect(intersection_analytes, plate$analyte_names)
}

if (length(intersection_analytes) == length(all_analyte_names)) {
  warning("Not all plates contain the same analytes. The report will contain only the analytes that are present in all plates. Number of all analytes: ",
          length(all_analyte_names),
          ". Number of common analytes: ",
          length(intersection_analytes))
}

analyte_names <- intersection_analytes


if (!is.null(additional_notes) && !is(additional_notes, "character")) {
  stop("The `additional_notes` must be a character value.")
}

date_of_first_plate <- min(sapply(list_of_plates, function(plate) plate$plate_datetime))
date_of_last_plate <- max(sapply(list_of_plates, function(plate) plate$plate_datetime))

# i need to add this trick otherwise i get error in format function
# Error in prettyNum(.Internal(format(x, trim, digits, nsmall, width, 3L,  :
#  invalid 'trim' argument
# it may cause some problems with timezones
# but few hours difference is not a big deal
date_of_first_plate <- as.POSIXct(date_of_first_plate,
                                  origin = "1970-01-01",
                                  tz = "UTC")
date_of_last_plate <- as.POSIXct(date_of_last_plate,
                                 origin = "1970-01-01",
                                 tz = "UTC")
time_span <- difftime(date_of_last_plate, date_of_first_plate, units = "days")

Report generated on: r format(Sys.time(), "%d-%m-%Y %H:%M:%S").
First plate was run on: r if(!is.null(date_of_first_plate)) format(date_of_first_plate, "%d-%m-%Y %H:%M") else "Date of running plate was not found in Luminex file".
Last plate was run on: r if(!is.null(date_of_last_plate)) format(date_of_last_plate, "%d-%m-%Y %H:%M") else "Date of running plate was not found in Luminex file".
Time span: r if(!is.null(time_span)) paste0(round(time_span, 2), " days") else "Dates were not found in Luminex file".
Number of plates used in report: r length(list_of_plates).
Plates have r paste0(length(analyte_names), " analytes").
Standard curve sample dilutions: r format_dilutions(list_of_plates[[1]]$dilutions, list_of_plates[[1]]$dilution_values, list_of_plates[[1]]$sample_types).

---

r if(!is.null(additional_notes)) "### Additional notes \n"

r if(!is.null(additional_notes)) additional_notes

r if(!is.null(additional_notes)) "\n -------------------"

Plates used in this report

Click to show/hide list

for (plate in list_of_plates) {
  cat(paste0("- ", plate$plate_name, "\n"))
}

Plate layout

Click to show/hide layout

plot_layout(list_of_plates[[1]])

---

Details for given analyte {.tabset .tabset-fade}

# Code used to create dynamic tabs based on the number of analytes
for (i in seq_along(analyte_names)) {
  cat(paste0("#### ", analyte_names[i], "\n"))

  # Plot stacked curves monochromatic
  print(plot_standard_curve_stacked(list_of_plates, analyte_names[i]))

  # Plot stacked curves colored
  print(plot_standard_curve_stacked(list_of_plates,
                                    analyte_names[i],
                                    monochromatic = FALSE))

  for (dilution in params$dilutions) {
    # Plot levey-jennings
    print(plot_levey_jennings(list_of_plates, analyte_names[i], dilution))
  }

  cat("\n\n")
}

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Generated using the SerolyzeR package

SerolyzeR documentation built on April 12, 2025, 2:11 a.m.