RastaRocket (version 1.0.2)

plot_volcano: Volcano Plot for Adverse Event Analysis

Description

Generates a volcano plot to visualize the association between adverse events and patient groups.

Usage

plot_volcano(
  df_pat_grp,
  df_pat_llt,
  ref_grp = NULL,
  colors_arm = c("#1b9e77", "#7570b3"),
  size = "nb_pat"
)

Value

A ggplot2 object representing the volcano plot.

Arguments

df_pat_grp

A data frame of patient groups. Must contain columns USUBJID (patient ID) and RDGRPNAME (group assignment).

df_pat_llt

A data frame with USUBJID (subject ID), EINUM (AE ID), EILLTN (LLT identifier), EIPTN (PT identifier), EISOCPN (soc identifier) and EIGRDM (severity grade)

ref_grp

(Optional) A reference group for comparisons. Defaults to the first group in df_pat_grp.

colors_arm

A character vector of length two specifying the colors for the two patient groups in the plot. Default is c("#1b9e77", "#7570b3").

size

A character string specifying the metric used for point sizes in the plot. Options are:

• "nb_pat": Number of patients (default).

• "nb_ei": Number of adverse events.

Details

The function first processes input data using df_builder_ae(), then calculates relevant statistics such as risk difference (RD) and p-values. The volcano plot displays:

• RD on the x-axis (risk difference between groups).

• -log10(p-value) on the y-axis (significance level).

• Point colors indicating which group has an increased risk.

• Point sizes reflecting either the number of patients or events.

• A horizontal dashed line at p = 0.05 for significance threshold.

Examples

df_pat_grp <- data.frame(
 USUBJID = paste0("ID_", 1:10),
 RDGRPNAME = c(rep("A", 5), rep("B", 5))
)

df_pat_llt <- data.frame(
  USUBJID = c("ID_1", "ID_1", "ID_2", "ID_4", "ID_9"),
  EINUM = c(1, 2, 1, 1, 1),
  EILLTN = c("llt1", "llt2", "llt1", "llt3", "llt4"),
  EIPTN = c("Arrhythmia", "Myocardial Infarction", "Arrhythmia", "Pneumonia", "Pneumonia"),
  EISOCPN = c("Cardiac Disorders", "Cardiac Disorders", "Cardiac Disorders",
  "Infections", "Infections"),
  EIGRDM = c(1, 3, 4, 2, 4)
)

plot_volcano(df_pat_grp, df_pat_llt)