% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocessingMinfiEwasWater_steps.R
\name{plotAssessmentMinfiEwasWater}
\alias{plotAssessmentMinfiEwasWater}
\title{Plot quality-assessment outputs for preprocessingMinfiEwasWater}
\usage{
plotAssessmentMinfiEwasWater(
  assessment,
  plot = c("qc", "detection"),
  display = FALSE,
  file = NULL,
  width = 2000L,
  height = 1000L,
  res = 150L,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_plotAssessmentMinfiEwasWater.txt"
)
}
\arguments{
\item{assessment}{Object returned by \code{assessSamplesMinfiEwasWater()}.}

\item{plot}{Character. Plot type: \code{'qc'} or \code{'detection'}.}

\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 either the minfi QC plot or the detection P-value plot from an
assessment object returned by \code{assessSamplesMinfiEwasWater()}.
}
\examples{
assessment <- list(
    meanDetP = c(S1 = 0.01, S2 = 0.02, S3 = 0.04),
    detPThreshold = 0.05
)
plotAssessmentMinfiEwasWater(
    assessment = assessment,
    plot = "detection",
    display = FALSE,
    verbose = FALSE,
    logs = FALSE
)

}
