Plot MassGLM using volcano plot

Usage

# S3 method for class 'MassGLM'
plot(
  x,
  coefname = NULL,
  p_adjust_method = "holm",
  p_transform = function(x) -log10(x),
  xlab = "Coefficient",
  ylab = NULL,
  theme = choose_theme(getOption("rtemis_theme")),
  verbosity = 1L,
  ...
)

Arguments

x: MassGLM object trained using massGLM.
coefname: Character: Name of coefficient to plot. If NULL, the first coefficient is used.
p_adjust_method: Character: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" - p-value adjustment method.
p_transform: Function to transform p-values for plotting. Default is function(x) -log10(x).
xlab: Character: x-axis label.
ylab: Character: y-axis label.
theme: Theme object. Create using one of the theme_ functions, e.g. theme_whitegrid().
verbosity: Integer: Verbosity level.
...: Additional arguments passed to draw_volcano.

Author

EDG

Examples

if (FALSE) { # interactive()
set.seed(2019)
y <- rnormmat(500, 500, return_df = TRUE)
x <- data.frame(x = y[, 3] + y[, 5] - y[, 9] + y[, 15] + rnorm(500))
mod <- massGLM(x, y)
plot(mod)
}