Standard curve stacked plot for levey-jennings report — plot_standard_curve

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
)
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_1_xponent.csv
#> using format xPONENT
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IM p
#> 
#> New plate object has been created with name: IGG_CO_1_xponent!
#> 
#> Processing plate 'IGG_CO_1_xponent'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_1_xponent_MFI.csv already exists. Overwriting it.
#> Extracting the raw MFI to the output dataframe
#> Saving the computed MFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_1_xponent_MFI.csv'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_1_xponent_RAU.csv already exists. Overwriting it.
#> Fitting the models and predicting RAU for each analyte
#> Saving the computed RAU values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_1_xponent_RAU.csv'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_1_xponent_nMFI.csv already exists. Overwriting it.
#> Computing nMFI values for each analyte
#> Saving the computed nMFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_1_xponent_nMFI.csv'
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_2_xponent.csv
#> using format xPONENT
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IM p
#> 
#> New plate object has been created with name: IGG_CO_2_xponent!
#> 
#> Processing plate 'IGG_CO_2_xponent'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_2_xponent_MFI.csv already exists. Overwriting it.
#> Extracting the raw MFI to the output dataframe
#> Saving the computed MFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_2_xponent_MFI.csv'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_2_xponent_RAU.csv already exists. Overwriting it.
#> Fitting the models and predicting RAU for each analyte
#> Saving the computed RAU values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_2_xponent_RAU.csv'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_2_xponent_nMFI.csv already exists. Overwriting it.
#> Computing nMFI values for each analyte
#> Saving the computed nMFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_2_xponent_nMFI.csv'
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_3_xponent.csv
#> using format xPONENT
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IM p
#> 
#> New plate object has been created with name: IGG_CO_3_xponent!
#> 
#> Processing plate 'IGG_CO_3_xponent'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_3_xponent_MFI.csv already exists. Overwriting it.
#> Extracting the raw MFI to the output dataframe
#> Saving the computed MFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_3_xponent_MFI.csv'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_3_xponent_RAU.csv already exists. Overwriting it.
#> Fitting the models and predicting RAU for each analyte
#> Saving the computed RAU values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_3_xponent_RAU.csv'
#> Warning: The specified file /tmp/Rtmpl5e8H2/IGG_CO_3_xponent_nMFI.csv already exists. Overwriting it.
#> Computing nMFI values for each analyte
#> Saving the computed nMFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/IGG_CO_3_xponent_nMFI.csv'
plot_standard_curve_stacked(list_of_plates, "ME", data_type = "Median", monochromatic = FALSE)