generate_plate_report {SerolyzeR} | R Documentation |
Generate a report for a plate.
Description
This function generates a report for a plate. The report contains all the necessary information about the plate, from the general plate parameters, such as examination date, to the breakdown of the analytes' plots.
The report is generated using the R Markdown template file
plate_report_template.Rmd
, located in the
inst/templates
directory of the package. You can access it using:
system.file("templates/plate_report_template.Rmd", package = "SerolyzeR")
.
Usage
generate_plate_report(
plate,
use_model = TRUE,
filename = NULL,
output_dir = "reports",
counts_lower_threshold = 50,
counts_higher_threshold = 70,
additional_notes = NULL,
...
)
Arguments
plate |
A plate object. |
use_model |
( |
filename |
( If the passed filename does not contain |
output_dir |
( |
counts_lower_threshold |
( |
counts_higher_threshold |
( |
additional_notes |
( |
... |
Additional params passed to the plots created in the report. |
Value
A report.
Examples
plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "SerolyzeR")
# a plate file with reduced number of analytes to speed up the computation
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "SerolyzeR")
note <- "This is a test report.\n**Author**: Jane Doe \n**Tester**: John Doe"
plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)
example_dir <- tempdir(check = TRUE) # a temporary directory
generate_plate_report(plate,
output_dir = example_dir,
counts_lower_threshold = 40,
counts_higher_threshold = 50,
additional_notes = note
)