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Generate a General Line Plot for ADNCA Dataset

Source: R/general_lineplot.R
general_lineplot.Rd

This function generates a line plot for an ADNCA dataset based on user-selected analytes, subjects, and other parameters. The plot can be customized to display data on a linear or logarithmic scale and can be filtered by cycle.

Usage

general_lineplot(
  data,
  selected_analytes,
  selected_pcspec,
  selected_usubjids,
  colorby_var = "USUBJID",
  facet_by = NULL,
  time_scale,
  yaxis_scale,
  show_threshold = FALSE,
  threshold_value = 0,
  show_dose = FALSE,
  cycle = NULL,
  palette = NULL
)

Arguments

data

A data frame containing the ADNCA dataset.

selected_analytes

A character vector of selected analytes to be included in the plot.

selected_pcspec

A character vector of selected matrix to be included in the plot.

selected_usubjids

A character vector of selected unique subject identifiers (USUBJIDs) to be included in the plot.

colorby_var

A character string specifying the variable by which to color the lines in the plot.

facet_by

A character vector specifying the variables by which to facet the plot.

time_scale

A character string specifying the time scale. Options are "By Cycle" or other values.

yaxis_scale

A character string specifying the x-axis scale. Options are "Log" or other values.

show_threshold

A boolean specifying whether to show a threshold line or not. Default is FALSE.

threshold_value

A numeric value to set the y value of the threshold line. Default is 0.

show_dose

A boolean specifying whether to show dose times as vertical lines.

cycle

A character string or numeric value specifying the cycle to filter by when time_scale is "By Cycle". Default is NULL.

palette

Specification of the color palette to use for the plot.

Value

A ggplot object representing the line plot of pharmacokinetic concentration over time.

Details

The function performs the following steps:a

  • Filters the data based on the selected analytes, matrices, and subjects.

  • Selects relevant columns and removes rows with missing concentration values.

  • Converts 'USUBJID', 'ATPTREF', and 'DOSEA' to factors.

  • Filters the data by cycle if time_scale is "By Cycle" while creating duplicates for predose samples if needed.

  • Adjusts concentration values for logarithmic scale if yaxis_scale is "Log".

  • Generates a line plot using the g_ipp function with the specified parameters.

  • Adjusts the y-axis to logarithmic scale if yaxis_scale is "Log".

  • Adds a horizontal line for the threshold value if show_threshold is TRUE.

  • Adds vertical lines for dose times if show_dose is TRUE and the number of subjects is less than 5.

Examples

adnca <- read.csv(system.file("shiny/data/example-ADNCA.csv", package = "aNCA"))
# Use actual values from the dummy data for the example
selected_analytes <- head(unique(adnca$ANALYTE), 1)
selected_pcspec <- head(unique(adnca$PCSPEC), 1)
selected_usubjids <- head(unique(adnca$USUBJID), 1)
plot <- general_lineplot(
  data = adnca,
  selected_analytes = selected_analytes,
  selected_pcspec = selected_pcspec,
  selected_usubjids = selected_usubjids,
  colorby_var = "ATPTREF",
  time_scale = "By Cycle",
  yaxis_scale = "Log",
  cycle = "1",
  show_threshold = TRUE,
  threshold_value = 1
)
print(plot)