Median Fluorescent Intensity (MFI) Box Plots

Boxplot of the MFI values.

Usage

plotMFI(mfi_to_rau_output, location)

Arguments

mfi_to_rau_output

Output from `MFItoRAU()` or `MFItoRAU_Adj()` .

location

"PNG" or "ETH".

Value

Box plots with MFI values for each protein (ggplot).

Author

Dionne Argyropoulos

Examples

# \donttest{

# Step 0: Load example raw data
your_raw_data <- c(
  system.file("extdata", "example_MAGPIX_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_plate2.csv", package = "SeroTrackR")
)
your_plate_layout <- system.file(
  "extdata",
  "example_platelayout_1.xlsx",
  package = "SeroTrackR"
)

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

# Step 2: Process counts and perform quality control
qc_results <- runQC(sero_data, plate_list)

# Step 3: Convert MFI to RAU using ETH beads
mfi_to_rau <- MFItoRAU_Adj(
  sero_data   = sero_data,
  plate_list  = plate_list,
  qc_results  = qc_results
)
#> Joining with `by = join_by(antigen)`
#> Joining with `by = join_by(antigen)`
#> Joining with `by = join_by(antigen)`
#> Joining with `by = join_by(antigen)`
#> Joining with `by = join_by(antigen)`
#> Joining with `by = join_by(antigen)`

# Step 4: Plot MFI values
plotMFI(mfi_to_rau, "MFI")
#> Warning: Removed 1094 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 79 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).

# }