% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/plots.R

\name{volcano_ic}

\alias{volcano_ic}

\title{Volcano plot for class biotmle}

\usage{

volcano_ic(biotmle, ate_bound = 1, pval_bound = 0.2)

}

\arguments{

\item{biotmle}{object of class \code{biotmle} as produced by an appropriate

call to \code{biomarkertmle}}

\item{ate_bound}{A \code{numeric} indicating the highest magnitude of the

average treatment effect to be colored on the x-axis of the volcano plot;

this limits the observations to be considered differentially expressed to

those in a user-specified interval.}

\item{pval_bound}{A \code{numeric} indicating the largest corrected p-value

to be colored on the y-axis of the volcano plot; this limits observations

considered as differentially expressed to those in a user-specified

interval.}

}

\value{

object of class \code{ggplot} containing a standard volcano plot of

 the log-fold change in the causal target parameter against the raw log

 p-value computed from the moderated tests in \code{modtest_ic}.

}

\description{

Volcano plot of the log-changes in the target causal paramter against the

log raw p-values from the moderated t-test.

}

\examples{

\dontrun{

library(dplyr)

library(biotmleData)

library(SuperLearner)

library(SummarizedExperiment)

data(illuminaData)

colData(illuminaData) <- colData(illuminaData) \%>\%

  data.frame() \%>\%

  mutate(age = as.numeric(age > median(age))) \%>\%

  DataFrame()

benz_idx <- which(names(colData(illuminaData)) \%in\% "benzene")

biomarkerTMLEout <- biomarkertmle(

  se = illuminaData,

  varInt = benz_idx,

  bppar_type = BiocParallel::SerialParam(),

  g_lib = c("SL.mean", "SL.glm"),

  Q_lib = c("SL.mean", "SL.glm")

)

limmaTMLEout <- modtest_ic(biotmle = biomarkerTMLEout)

volcano_ic(biotmle = limmaTMLEout)

}

}