plot_standard_curve_stacked: Standard curve stacked plot for levey-jennings report

In SerolyzeR: Reading, Quality Control and Preprocessing of MBA (Multiplex Bead Assay) Data

Standard curve stacked plot for levey-jennings report

Description

Function generates a plot of stacked on top of each other standard curves for a given analyte form a list of plates. The plot is created with the levey-jennings report in mind, but it can be run by itself.

Usage

plot_standard_curve_stacked(
  list_of_plates,
  analyte_name,
  data_type = "Median",
  decreasing_dilution_order = TRUE,
  monochromatic = TRUE,
  legend_type = NULL,
  log_scale = c("all"),
  verbose = TRUE
)

Arguments

list_of_plates	list of Plate objects
analyte_name	Name of the analyte of which standard curves we want to plot.
data_type	Data type of the value we want to plot - the same datatype as in the plate file. By default equals to Median
decreasing_dilution_order	If TRUE the dilution values are plotted in decreasing order, TRUE by default
monochromatic	If TRUE the color of standard curves changes from white (the oldest) to blue (the newest) it helps to observe drift in calibration of the device; otherwise, more varied colours are used, TRUE by default
legend_type	default value is NULL, then legend type is determined based on monochromatic value. If monochromatic is equal to TRUE then legend type is set to date, if it is FALSE then legend type is set to plate_name. User can override this behavior by setting explicitly legend_type to date or plate_name.
log_scale	Which elements on the plot should be displayed in log scale. By default "all". If NULL or c() no log scale is used, if "all" or c("dilutions", "MFI") all elements are displayed in log scale.
verbose	If TRUE prints messages, TRUE by default

Value

ggplot object with the plot

Examples

# creating temporary directory for the example
output_dir <- tempdir(check = TRUE)

dir_with_luminex_files <- system.file("extdata", "multiplate_reallife_reduced",
  package = "SerolyzeR", mustWork = TRUE
)
list_of_plates <- process_dir(dir_with_luminex_files,
  return_plates = TRUE, format = "xPONENT", output_dir = output_dir
)
plot_standard_curve_stacked(list_of_plates, "ME", data_type = "Median", monochromatic = FALSE)

SerolyzeR documentation built on April 12, 2025, 2:11 a.m.