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Individual Patient Plots

Source: R/individual_patient_plot.R
individual_patient_plot.Rd

[Stable]

Usage 

h_set_nest_theme(font_size)

h_g_ipp(
  df,
  xvar,
  yvar,
  xlab,
  ylab,
  id_var,
  title = "Individual Patient Plots",
  subtitle = "",
  caption = NULL,
  add_baseline_hline = FALSE,
  yvar_baseline = "BASE",
  ggtheme = nestcolor::theme_nest(),
  col = NULL
)

g_ipp(
  df,
  xvar,
  yvar,
  xlab,
  ylab,
  id_var = "USUBJID",
  title = "Individual Patient Plots",
  subtitle = "",
  caption = NULL,
  add_baseline_hline = FALSE,
  yvar_baseline = "BASE",
  ggtheme = nestcolor::theme_nest(),
  plotting_choices = c("all_in_one", "split_by_max_obs", "separate_by_obs"),
  max_obs_per_plot = 4,
  col = NULL
)

Arguments

font_size

(number)
text font size.

df

(data frame)
data set containing all analysis variables.

xvar

(string)
time point variable to be plotted on x-axis.

yvar

(string)
continuous analysis variable to be plotted on y-axis.

xlab

(string)
plot label for x-axis.

ylab

(string)
plot label for y-axis.

id_var

(string)
variable used as patient identifier.

title

(string)
title for plot.

subtitle

(string)
subtitle for plot.

caption

(character scalar)
optional caption below the plot.

add_baseline_hline

(flag)
adds horizontal line at baseline y-value on plot when TRUE.

yvar_baseline

(string)
variable with baseline values only. Ignored when add_baseline_hline is FALSE.

ggtheme

(theme)
optional graphical theme function as provided by ggplot2 to control outlook of plot. Use ggplot2::theme() to tweak the display.

col

(character)
lines colors.

plotting_choices

(character)
specifies options for displaying plots. Must be one of "all_in_one", "split_by_max_obs", "separate_by_obs".

max_obs_per_plot

(count)
Number of observations to be plotted on one plot. Ignored when plotting_choices is not "separate_by_obs".

Value

a ggplot object or a list of ggplot objects.

Details

Line plot(s) displaying trend in patients' parameter values over time is rendered. Patients' individual baseline values can be added to the plot(s) as reference.

Functions

  • h_set_nest_theme(): sets a ggplot graphical theme to control outlook of plot.

  • h_g_ipp(): helper function that generates a simple line plot displaying parameter trends over time.

  • g_ipp(): depending on user preference, renders a single graphic or compiles a list of graphics that show trends in individual's parameter values over time.

Examples 


library(scda)
library(dplyr)
library(nestcolor)

# Select a small sample of data to plot.
adlb <- synthetic_cdisc_data("latest")$adlb %>%
  filter(PARAMCD == "ALT", !(AVISIT %in% c("SCREENING", "BASELINE"))) %>%
  slice(1:36)

p <- h_g_ipp(
  df = adlb,
  xvar = "AVISIT",
  yvar = "AVAL",
  xlab = "Visit",
  id_var = "USUBJID",
  ylab = "SGOT/ALT (U/L)",
  add_baseline_hline = TRUE
)
p


plot_list <- g_ipp(
  df = adlb,
  xvar = "AVISIT",
  yvar = "AVAL",
  xlab = "Visit",
  ylab = "SGOT/ALT (U/L)",
  title = "Individual Patient Plots",
  add_baseline_hline = TRUE,
  plotting_choices = "split_by_max_obs",
  max_obs_per_plot = 5
)
plot_list
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