% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/methylationGLM_steps.R
\name{plotMethylationGLMDistributions}
\alias{plotMethylationGLMDistributions}
\title{Plot phenotype and covariate distributions for one-timepoint GLM analyses}
\usage{
plotMethylationGLMDistributions(
  preparedData,
  plotWidth = 2000L,
  plotHeight = 1000L,
  plotDPI = 150L,
  outputDir = NULL,
  display = FALSE,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationGLM.txt"
)
}
\arguments{
\item{preparedData}{Object returned by \code{prepareMethylationGLMData()}.}

\item{plotWidth}{Integer. TIFF width in pixels when plots are written to
disk.}

\item{plotHeight}{Integer. TIFF height in pixels when plots are written to
disk.}

\item{plotDPI}{Integer. TIFF resolution in DPI when plots are written to
disk.}

\item{outputDir}{Character or \code{NULL}. Directory used for TIFF files. When
\code{NULL}, plots are returned in memory only.}

\item{display}{Logical. If \code{TRUE}, draw plots on the active graphics device.}

\item{verbose}{Logical. If \code{TRUE}, emit progress messages with \code{message()}.}

\item{logs}{Logical. If \code{TRUE}, write the same messages to a log file.}

\item{log_dir}{Character or \code{NULL}. Directory used for the log file when
\code{logs = TRUE}.}

\item{log_file}{Character. File name used when \code{logs = TRUE}.}
}
\value{
A list with class \code{'dnaEPICO_methylationGLM_distribution_plots'}
containing the generated \code{ggplot2} objects and any saved TIFF file paths.
}
\description{
Create phenotype, factor-variable, and numeric-covariate distribution plots
from the object returned by \code{prepareMethylationGLMData()}.
}
\examples{
ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
distribution_plots <- plotMethylationGLMDistributions(
    preparedData = ex$preparedData,
    display = FALSE,
    verbose = FALSE,
    logs = FALSE
)
names(distribution_plots)

}
