Dot plot

Create a dot plot by item. For instance, this could be used to create AEs incidence plot by Preferred Term and treatment group, as part of a rainfall plot.

Usage

plot_dot(
  tbl,
  prop_cols = c("prop_1", "prop_2"),
  y_var,
  label,
  x_breaks = NULL,
  color = NULL,
  shape = NULL,
  title = "AE (%)",
  background_color = c("#69B8F7", "#FFFFFF"),
  background_alpha = 0.3,
  theme = theme_panel(show_text = TRUE, show_ticks = TRUE),
  legend_nrow = 1
)

Arguments

tbl

A data frame selected from input data set to display on this plot. y and x variables are required.

prop_cols

A character vector of proportion columns to be used for a plot.

y_var

A character string that specifies a variable to be displayed on the y-axis.

label

A character vector of labels for each treatment group. The control group label should be specified as the last element of the vector.

x_breaks

A numeric vector for x-axis breaks. Default is NULL, which uses a default ggplot2 x-axis breaks presentation.

color

Color for each treatment group.

shape

Shape for each treatment group. Default is circle and square. Input values could be either a character or numeric value, For details, see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html.

title

Panel title. Default is "AE (%)".

background_color

Plot background color. Default is c("#69B8F7", "#FFFFFF"), which are pastel blue and white. The value of this argument is used as input for the background_color argument in background_panel().

background_alpha

Opacity of the background. Default is 0.3. The value of this argument is the input for background_alpha argument in background_panel().

theme

Panel theme, including the y-axis text, ticks, and plot margin. Default is theme_panel(show_text = TRUE, show_ticks = TRUE). For more details, refer to theme_panel.

legend_nrow

Integer, the number of rows for a legend display. Must be smaller than or equal to the number of the treatment groups. To omit the legend, set this to NULL. Default is 1.

Value

AEs incidence plot by item and treatment group.

Examples

forestly_adsl$TRTA <- factor(
  forestly_adsl$TRT01A,
  levels = c("Xanomeline Low Dose", "Placebo"),
  labels = c("Low Dose", "Placebo")
)
forestly_adae$TRTA <- factor(
  forestly_adae$TRTA,
  levels = c("Xanomeline Low Dose", "Placebo"),
  labels = c("Low Dose", "Placebo")
)

analysis_plan <- metalite::plan(
  analysis = "ae_forestly",
  population = "apat",
  observation = "wk12",
  parameter = "any"
)
meta <- metalite::meta_adam(
  population = forestly_adsl,
  observation = forestly_adae
) |>
  metalite::define_plan(plan = analysis_plan) |>
  metalite::define_population(
    name = "apat",
    var = c("USUBJID", "SAFFL", "TRTA", "SITEID", "SEX", "RACE", "AGE"),
    group = "TRTA",
    subset = SAFFL == "Y",
    label = "All Participants as Treated"
  ) |>
  metalite::define_observation(
    name = "wk12",
    var = c(
      "USUBJID", "SAFFL", "TRTA", "SITEID", "SEX", "RACE", "AGE",
      "ASTDY", "AEDECOD", "AEBODSYS", "AESER", "AEREL", "AEACN",
      "AEOUT", "ADURN", "ADURU"
    ),
    group = "TRTA",
    subset = SAFFL == "Y",
    label = "Weeks 0 to 12"
  ) |>
  metalite::define_parameter(
    name = "any",
    term1 = "",
    term2 = "",
    var = "AEDECOD",
    soc = "AEBODSYS",
    label = "All AEs"
  ) |>
  metalite::define_analysis(
    name = "ae_forestly",
    label = "Interactive forest plot"
  ) |>
  metalite::meta_build()

outdata <- meta |>
  prepare_ae_forestly(parameter = "any") |>
  format_ae_forestly()

outdata_any <- outdata$tbl[1:20, ] |> dplyr::filter(parameter == "any")
outdata_any |>
  plot_dot("name", prop_cols = c("prop_1", "prop_2"), label = c("Treatment", "Placebo"))
#> Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the forestly package.
#>   Please report the issue at <https://github.com/Merck/forestly/issues>.