Generate a Levey-Jennings Report for Multiple Plates. — generate_levey_jennings

This function generates a Levey-Jennings report for a list of plates. The report includes layout plot, levey jennings plot, for each analyte and selected dilutions.

Usage

generate_levey_jennings_report(
  list_of_plates,
  report_title,
  dilutions = c("1/100", "1/400"),
  filename = NULL,
  output_dir = "reports",
  additional_notes = NULL,
  ...
)

Arguments

list_of_plates: A list of plate objects.
report_title: (character(1)) The title of the report.
dilutions: (character) A character vector specifying the dilutions to be included in the report. Default is c("1/100", "1/400").
filename: (character(1)) The name of the output HTML report file. If not provided or set to NULL, the filename will be based on the first plate name, formatted as {plate_name}_levey_jennings.html. If the filename does not contain the .html extension, it will be automatically added. Absolute file paths in filename will override output_dir. Existing files at the specified path will be overwritten.
output_dir: (character(1)) The directory where the report will be saved. Defaults to 'reports'. If NULL, the current working directory will be used. Necessary directories will be created if they do not exist.
additional_notes: (character(1)) Additional notes to be included in the report. Markdown formatting is supported. If not provided, the section will be omitted.
...: Additional params passed to the plots created within the report.

Value

A Levey-Jennings report in HTML format.

Details

The report also includes stacked standard curves plot in both monochromatic and color versions for each analyte. The report is generated using the R Markdown template file levey_jennings_report_template.Rmd, located in the inst/templates directory of the package. You can access it using: system.file("templates/levey_jennings_report_template.Rmd", package = "SerolyzeR").

Examples

output_dir <- tempdir(check = TRUE)

dir_with_luminex_files <- system.file("extdata", "multiplate_lite",
  package = "SerolyzeR", mustWork = TRUE
)
list_of_plates <- process_dir(dir_with_luminex_files,
  return_plates = TRUE, format = "xPONENT", output_dir = output_dir
)
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/multiplate_lite/CovidOISExPONTENT.csv
#> using format xPONENT
#> Failed to extract from BatchMetadata: BatchStartTime not found in BatchMetadata.
#> Failed to extract from raw header: BatchStartTime not found in raw header.
#> Fallback datetime successfully extracted from ProgramMetadata.
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IM p
#> 
#> New plate object has been created with name: CovidOISExPONTENT!
#> 
#> Processing plate 'CovidOISExPONTENT'
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/multiplate_lite/CovidOISExPONTENT2.csv
#> using format xPONENT
#> Failed to extract from BatchMetadata: BatchStartTime not found in BatchMetadata.
#> Failed to extract from raw header: BatchStartTime not found in raw header.
#> Fallback datetime successfully extracted from ProgramMetadata.
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IM p
#> 
#> New plate object has been created with name: CovidOISExPONTENT2!
#> 
#> Processing plate 'CovidOISExPONTENT2'
#> Extracting the raw MFI to the output dataframe
#> Extracting the raw MFI to the output dataframe
#> Merged output saved to: /tmp/RtmpRMSIkp/merged_MFI_20250718_180143.csv
#> Fitting the models and predicting RAU for each analyte
#> Fitting the models and predicting RAU for each analyte
#> Merged output saved to: /tmp/RtmpRMSIkp/merged_RAU_20250718_180143.csv
#> Computing nMFI values for each analyte
#> Computing nMFI values for each analyte
#> Merged output saved to: /tmp/RtmpRMSIkp/merged_nMFI_20250718_180143.csv
note <- "This is a Levey-Jennings report.\n**Author**: Jane Doe \n**Tester**: John Doe"

generate_levey_jennings_report(
  list_of_plates = list_of_plates,
  report_title = "QC Report",
  dilutions = c("1/100", "1/200"),
  output_dir = tempdir(),
  additional_notes = note
)
#> Generating report... For large reports with more than 30 plates, this will take a few minutes.
#> Report successfully generated, saving to: /tmp/RtmpRMSIkp/CovidOISExPONTENT_levey_jennings.html