PKbioanalysis overview

Omar Elashkar

library(PKbioanalysis)

Plate generation, reusing and managing plates

plate <- generate_96() 
plot(plate)
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 96 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Calibration study examples

plate <- generate_96("Calibration study") |> 
    add_cs_curve(c(1, 3, 5, 10, 20, 50, 100, 200, 500)) |>
    add_DB() |> 
    add_DB() |>
    add_blank() |>   # CS0IS1
    add_suitability(conc = 20) |>
    add_qcs(2, 200 ,400, qc_serial = FALSE) |> 
    add_DB() |> 
    add_blank(analyte = TRUE, IS = FALSE) |> # CS1IS0
    add_cs_curve(c(1, 3, 5, 10, 20, 50, 100, 200, 500)) |>
    add_qcs(lqc_conc = 2, mqc_conc =  180 , hqc_conc = 400) 

plot(plate)
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 48 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "TYPE")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 48 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plate <- register_plate(plate)
plot(plate)
plate <- generate_96() |> 
    add_suitability(conc = 10) |>
    make_calibration_study(
        plate_std = c(1, 3, 5, 10, 20, 50, 100, 200, 500), 
        lqc_conc = 2, 
        mqc_conc = 40,
        hqc_conc = 100, 
        n_qc = 4, 
        qc_serial = TRUE, 
        n_CS0IS0 = 2,
        n_CS1IS0 = 2,
        n_CS0IS1 = 2)
plot(plate, color = "TYPE")
plot(plate, color  = "conc")
plate <- register_plate(plate)
plate_app()

Adding samples

plate <- generate_96() |> add_samples(1:20)

plot(plate)
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 76 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Adding samples manually or from external spreadsheet

plate <- generate_96()

plate <- plate |> 
    add_samples("sample1") |> 
    add_samples("sample2") |>
    add_samples("sample3")

plot(plate)
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 93 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Define samples by attributes

data(Indometh)
plate <- generate_96() |> 
    add_samples(samples = Indometh$Subject, 
                time = Indometh$time)
plot(plate, color = "time")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 30 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "samples")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 30 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Automated crossover

plate <- generate_96() |> 
    # add_samples_c(c("subject1", "subject2"), time = c(0, 10, 30, 60, 120), factor = "Male") |>
    add_samples_c("subject1", time = c(0, 10, 30, 60, 120), 
                  factor = "Male") |>
    add_samples_c("subject2", time =   c(0, 10, 30, 120), 
                  factor = "Female") 

plot(plate, color = "time")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 87 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "samples")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 87 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "factor")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 87 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "conc")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 87 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Food Effect Example

plate <- generate_96() |> 
    add_samples_c(1:4, time = c(0, 10, 30, 60, 120), 
         factor = c("Fed", "Fast"))
plot(plate, color = "time")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 56 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "samples")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 56 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "factor")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 56 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "conc")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 56 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Metabolic study (Multiple plates)

plates <- make_metabolic_study(
    cmpd = c("NE", "DA", "5HT", "HVA", 
             "DOPAC", "MHPG", "5HIAA", "VMA"),
    time_points = c(0, 5, 10, 15, 30, 45, 60, 90, 120),
    n_NAD = 3, 
    n_noNAD = 2
)
length(plates)
#> [1] 7
plot(plates[[1]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[2]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[3]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[4]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[5]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[6]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

register_plate(plates)