% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/svaEnmix_steps.R
\name{plotSvaEnmix}
\alias{plotSvaEnmix}
\title{Plot surrogate variables for svaEnmix}
\usage{
plotSvaEnmix(
  analysisData,
  plot = c("sentrix_id", "sentrix_position", "matrix"),
  display = FALSE,
  file = NULL,
  width = 2000L,
  height = 1000L,
  res = 150L,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_plotSvaEnmix.txt"
)
}
\arguments{
\item{analysisData}{Object returned by \code{analyzeSvaEnmix()}.}

\item{plot}{Character. Plot type: \code{'sentrix_id'}, \code{'sentrix_position'}, or
\code{'matrix'}.}

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

\item{file}{Character or \code{NULL}. TIFF file path used for saved output.}

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

\item{height}{Integer. Plot 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 saved TIFF path(s), otherwise \code{NULL}.
}
\description{
Draw one of the standard surrogate-variable plots used by \code{svaEnmix()}.
}
\examples{
ex <- dnaEPICO:::exampleSvaAnalysisStateDnaEpico()
plotSvaEnmix(
    analysisData = ex$analysisData,
    plot = "sentrix_id",
    display = FALSE,
    verbose = FALSE,
    logs = FALSE
)

}
