Read Plate Layout/s

This function imports the plate layout. Each sheet of the plate layout ".xlsx" file must contain 13 columns (labelled Plate, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12) (columns A-M) and 9 rows (Plate, A, B, C, D, E, F, G, H) (rows 1-9). *Note that the first row/column i.e., the A1 cell in excel is called "Plate". This function also checks that the plate sheet labels are consistent with the MAGPIX file input names, as a check prior to merging downstream.

Usage

readPlateLayout(plate_layout, sero_data)

Arguments

plate_layout

An ".xlsx" file with sheets labelled plate1, plate2... etc..

sero_data

Output from `readSeroData()`.

Value

A list of data frames, with each one representing an individual plate.

Author

Shazia Ruybal-Pesántez, Dionne Argyropoulos

Examples

# Example input files
your_raw_data <- c(
  system.file("extdata", "example_MAGPIX_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_plate2.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_plate3.csv", package = "SeroTrackR")
)

your_plate_layout <- system.file(
  "extdata",
  "example_platelayout_1.xlsx",
  package = "SeroTrackR"
)

# Step 1: Read and combine serological data
sero_data <- readSeroData(
  raw_data = your_raw_data,
  platform = "magpix"
)
#> PASS: File example_magpix_plate1.csv successfully validated.
#> PASS: File example_magpix_plate2.csv successfully validated.
#> PASS: File example_magpix_plate3.csv successfully validated.
# Step 2: Read plate layout
plate_list <- readPlateLayout(
  plate_layout = your_plate_layout,
  sero_data = sero_data
)
#> Plate layouts correctly identified!