Raport for plate: `r paste0('*', params$plate$plate_name, '*')`

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

if (is.null(params$plate)) {
  stop("The `plate` must be provided when rendering the document.")
}
if (is.null(params$use_model)) {
  stop("The `use_model` must be provided when rendering the document.")
}
if (is.null(params$counts_lower_threshold)) {
  stop("The `counts_lower_threshold` must be provided when rendering the document.")
}
if (is.null(params$counts_higher_threshold)) {
  stop("The `counts_higher_threshold` must be provided when rendering the document.")
}
if (!is(params$plate, "Plate")) {
  stop("The `plate` must be an instance of `Plate` class.")
}
if (!is(params$use_model, "logical")) {
  stop("The `use_model` must be a logical value.")
}
if (!is(params$counts_lower_threshold, "numeric")) {
  stop("The `counts_lower_threshold` must be a numeric value.")
}
if (!is(params$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").
Plate was run on: r if(!is.null(params$plate$plate_datetime)) format(params$plate$plate_datetime, "%d-%m-%Y %H:%M:%S") else "Date of running plate was not found in Luminex file".
Plate batch name: r if(!is.null(params$plate$batch_name)) params$plate$batch_name else "Batch name was not found in Luminex file".
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

Click to show/hide layout

plot_layout(params$plate)

---

Quick overview of standard curves

Click to show/hide overview

# Code used to create dynamic tabs based on the number of analytes
# Start a grid for the plots
cat('<div class="plot-grid">')

models_list <- list()
# Generate the clickable plots within the grid
for (i in seq_along(params$plate$analyte_names)) {
  # HTML structure for each plot with a clickable link
  cat(paste0('<div class="plot-container">',
             '<a href="#', tolower(params$plate$analyte_names[i]), '" role="tab" data-toggle="tab" aria-controls="', tolower(params$plate$analyte_names[i]), '" aria-expanded="false">'))
  # Generate the plot
  model <- create_standard_curve_model_analyte(params$plate, params$plate$analyte_names[i])
  models_list[[params$plate$analyte_names[i]]] <- model
  print(plot_standard_curve_thumbnail(params$plate, params$plate$analyte_names[i])) 
#  print(plot_standard_curve_analyte_with_model(params$plate, model, plot_legend = FALSE, #plot_asymptote = FALSE, plot_rau_bounds = FALSE))
  cat('</a></div>')
}
# Close the grid
cat('</div>')

---

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

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

  # Plot counts
  print(plot_counts(params$plate, params$plate$analyte_names[i], lower_threshold = params$counts_lower_threshold, higher_threshold = params$counts_higher_threshold))

  # Plot MFI
  print(plot_mfi_for_analyte(params$plate, params$plate$analyte_names[i], plot_type = "violin"))

  # Plot Standard Curve
  print(plot_standard_curve_analyte(params$plate, params$plate$analyte_names[i]))
  if (params$use_model) {
    model <- models_list[[params$plate$analyte_names[i]]]
    print(plot_standard_curve_analyte_with_model(params$plate, model))
  }

  cat("\n\n")
}

---

 

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Generated using the PvSTATEM package

PvSTATEM documentation built on April 4, 2025, 4:34 a.m.