Plot Antibody Data with Optional Antigen-Level Table or Time-Series Trend

This function generates a bar plot of SAB (Single Antigen Beads) or PRA (Panel-Reactive Antibody) results from a provided data frame or a file path. It can also plot MFI values over time.

Usage

plotAntibodies(
  result_file,
  type = "SAB",
  class = "I",
  plot_trend = FALSE,
  bead_cutoffs = NULL,
  highlight_threshold = 2000,
  vline_dates = NULL,
  add_table = TRUE,
  x_text_angle = 90,
  palette = "spectral",
  highlight_antigen = NULL,
  ...
)

plotSAB(..., type = "SAB")

plotPRA(..., type = "PRA")

Arguments

result_file: A data frame, a list of data frames (for trend plot), or a character string specifying the path to a file in CSV, XLS, or XLSX format.
type: Character. The type of assay, either "SAB" or "PRA". Defaults to "SAB".
class: Character. For PRA plots, the class of the assay, either "I" or "II". Defaults to "I".
plot_trend: Logical. If TRUE, a time-series plot is generated. Defaults to FALSE.
bead_cutoffs: Numeric vector. Cutoff values for categorizing MFI values. Defaults to `c(2000, 1000, 500, 250)` for SAB and `c(1500, 1000, 500, 250)` for PRA.
highlight_threshold: Numeric. MFI threshold for highlighting alleles in the trend plot. Defaults to 2000.
vline_dates: Vector of dates. Dates to draw vertical lines on the trend plot.
add_table: Logical. Whether to add the antigen-level information as a table to the bottom of the bar plot. Defaults to TRUE.
x_text_angle: Numeric. Angle for the antigen/allele text in the table. Defaults to 90.
palette: Character. A color palette name. Defaults to "spectral".
highlight_antigen: Character vector. Optional antigen(s) to highlight.
...: Additional arguments passed to the ggplot theme.

Value

A `ggplot` object.

Examples

# Plot SAB Class I data
plotAntibodies(deepMatchR_example[[1]], type = "SAB")


# Plot without table
plotAntibodies(deepMatchR_example[[1]], type = "SAB", add_table = FALSE)


# Plot SAB Class II data
plotAntibodies(deepMatchR_example[[2]], type = "SAB")