Generate Volcano Plot of Adverse Events from Risk values of treatment pairs

Usage

ae_volcano_plot(
  datain,
  axis_opts,
  legend_opts = list(label = "", pos = "bottom", dir = "horizontal"),
  xref = c(1, 0, 2),
  pvalue_sig = 0.05,
  interactive = "N"
)

Arguments

datain: (data.frame)
Input dataset containing statistics for treatment pairs from AE data, generated by risk_stat().
axis_opts: A list of axis specific options retrieved from plot_axis_opts() and ae_volcano_opts().
legend_opts: Legend styling option, a list containing label, pos(position) and dir (direction).
xref: (numeric)
Numeric vector, from ae_volcano_opts First value will be the main reference, all drawn vertically.
pvalue_sig: (numeric)
p-value cut-off, filter values with adjusted p less than this argument
interactive: Return interactive plot or static. Values: "Y"/"N".

Value

a ggplot object (volcano plot)

Details

It is recommended not to change pos and dir in legend_opts; additionally, these options are fixed for the case of interactive = Y and cannot be changed. xref must be of length 2 or more. Input datain from risk_stat() should only contain one treatment pair and not more.

Examples

data("adae")

ae_pre <- ae_pre_processor(
  datain = adae,
  obs_residual = 0,
  fmq_data = NA
)

ae_entry <- mentry(
  datain = ae_pre$data,
  subset = NA,
  byvar = "AEBODSYS",
  trtvar = "TRTA",
  trtsort = "TRTAN",
  subgrpvar = NA,
  trttotalyn = "N",
  add_grpmiss = "N",
  sgtotalyn = "N",
  pop_fil = "SAFFL"
)

ae_risk <- risk_stat(
  datain = ae_entry,
  a_subset = ae_pre$a_subset,
  summary_by = "Patients",
  eventvar = "AEDECOD",
  ctrlgrp = "Placebo",
  trtgrp = "Xanomeline High Dose",
  statistics = "Risk Ratio",
  alpha = 0.05,
  cutoff_where = "FREQ >5",
  sort_opt = "Ascending",
  sort_var = "Count"
)
#> mcatstat success

vaxis_opts <- ae_volcano_opts(
  ae_risk,
  "Control",
  "Exposure",
  pvalue_trans = "-log10"
)

axis_opts <- plot_axis_opts(
  ylinearopts = vaxis_opts$ylinearopts,
  yaxis_scale = vaxis_opts$yaxis_scale,
  xaxis_label = vaxis_opts$xaxis_label,
  yaxis_label = vaxis_opts$yaxis_label
)

ae_risk |>
  ae_volcano_plot(
    axis_opts = axis_opts,
    xref = vaxis_opts$xref
  )