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Plot Levey-Jennings chart

Source: R/plots-levey_jennings.R
plot_levey_jennings.Rd

The function plots a Levey-Jennings chart for the given analyte in the list of plates. The Levey-Jennings chart is a graphical representation of the data that enables the detection of outliers and trends. It is a quality control tool that is widely used in the laboratories across the world.

The method takes several parameters that can customise its output. Except for the required parameters (list_of_plates and analyte_name), the most significant optional ones are dilution and sd_lines.

The additional parameters can be used for improving the plots interpretability, by customizing the layout, y-scale, etc.

For better readibilty, the plot is zoomed out in the y-axis, by a factor of 1.5.

Usage

plot_levey_jennings(
  list_of_plates,
  analyte_name,
  dilution = "1/400",
  sd_lines = c(1, 2, 3),
  mfi_log_scale = TRUE,
  sort_plates = TRUE,
  plate_labels = "number",
  label_angle = 0,
  legend_position = "bottom",
  data_type = "Median"
)

Arguments

list_of_plates

A list of plate objects for which to plot the Levey-Jennings chart

analyte_name

(character(1)) the analyte for which to plot the Levey-Jennings chart

dilution

(character(1)) the dilution for which to plot the Levey-Jennings chart. The default is "1/400"

sd_lines

(numeric) the vector of coefficients for the standard deviation lines to plot, for example, c(1.96, 2.58) will plot four horizontal lines: mean +/- 1.96sd, mean +/- 2.58sd default is c(1, 2, 3) which will plot 6 lines in total

mfi_log_scale

(logical(1)) specifies if the MFI should be in the log10 scale. By default it equals to TRUE, which corresponds to plotting the chart in log10 scale.

sort_plates

(logical(1)) if TRUE sorts plates by the date of examination. If FALSE plots using the plate order as in input. TRUE by default.

plate_labels

(character(1)) controls x-axis labels. Can improve readibility of the plot. Takes the following values:

  • "numbers": shows the number of the plate,

  • "names": shows the plate names

  • "dates": shows the date of examination

label_angle

(numeric(1)) angle in degrees to rotate x-axis labels. Can improve readibility of the plot. Default: 0

legend_position

the position of the legend, a possible values are c(right, bottom, left, top, none). Is not used if plot_legend equals to FALSE.

data_type

(character(1)) the type of data used plot. The default is "Median"

Value

A ggplot object with the Levey-Jennings chart

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
#> Failed to extract from BatchMetadata: BatchStartTime not found in BatchMetadata.
#> Failed to extract from raw header: BatchStartTime not found in raw header.
#> Fallback datetime successfully extracted from ProgramMetadata.
#> 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'
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_2_xponent.csv
#> using format xPONENT
#> Failed to extract from BatchMetadata: BatchStartTime not found in BatchMetadata.
#> BatchStartTime successfully extracted from the header.
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IMS p
#> 
#> New plate object has been created with name: IGG_CO_2_xponent!
#> 
#> Processing plate 'IGG_CO_2_xponent'
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/multiplate_reallife_reduced/IGG_CO_3_xponent.csv
#> using format xPONENT
#> Failed to extract from BatchMetadata: BatchStartTime not found in BatchMetadata.
#> BatchStartTime successfully extracted from the header.
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IMS p
#> 
#> New plate object has been created with name: IGG_CO_3_xponent!
#> 
#> Processing plate 'IGG_CO_3_xponent'
#> Extracting the raw MFI to the output dataframe
#> Extracting the raw MFI to the output dataframe
#> Extracting the raw MFI to the output dataframe
#> Merged output saved to: /tmp/RtmpwCdw23/merged_MFI_20251015_105118.csv
#> Fitting the models and predicting RAU for each analyte
#> Fitting the models and predicting RAU for each analyte
#> Fitting the models and predicting RAU for each analyte
#> Merged output saved to: /tmp/RtmpwCdw23/merged_RAU_20251015_105118.csv
#> Computing nMFI values for each analyte
#> Computing nMFI values for each analyte
#> Computing nMFI values for each analyte
#> Merged output saved to: /tmp/RtmpwCdw23/merged_nMFI_20251015_105118.csv
list_of_plates <- rep(list_of_plates, 10) # since we have only 3 plates i will repeat them 10 times

plot_levey_jennings(list_of_plates, "ME", dilution = "1/400", sd_lines = c(0.5, 1, 1.96, 2.58))