% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocessingMinfiEwasWater_steps.R
\name{plotNormalizationMinfiEwasWater}
\alias{plotNormalizationMinfiEwasWater}
\title{Plot raw and normalized methylation distributions}
\usage{
plotNormalizationMinfiEwasWater(
  RGSet,
  normData,
  targets,
  sexColumn = "Sex",
  display = FALSE,
  file = NULL,
  width = 2000L,
  height = 1000L,
  res = 150L,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_plotNormalizationMinfiEwasWater.txt"
)
}
\arguments{
\item{RGSet}{An \code{RGChannelSet} aligned with \code{targets}.}

\item{normData}{Object returned by \code{normalizeMinfiEwasWater()}.}

\item{targets}{Filtered phenotype data aligned with \code{RGSet}.}

\item{sexColumn}{Character. Name of the phenotype column used to colour the
density curves.}

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

\item{file}{Character or \code{NULL}. TIFF file written when supplied.}

\item{width}{Integer. TIFF width in pixels when \code{file} is supplied.}

\item{height}{Integer. TIFF height in pixels when \code{file} is supplied.}

\item{res}{Integer. TIFF resolution in DPI when \code{file} is supplied.}

\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{
Invisibly returns the saved TIFF path when \code{file} is supplied,
otherwise \code{NULL}.
}
\description{
Draw the density comparison plot used to inspect raw versus normalized data.
}
\examples{
ex <- dnaEPICO:::exampleMinfiMetricsStateDnaEpico()
plotNormalizationMinfiEwasWater(
    RGSet = ex$beta,
    normData = ex$normData,
    targets = ex$targets,
    sexColumn = "Sex",
    display = FALSE,
    verbose = FALSE,
    logs = FALSE
)

}
