% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mhtplot.R
\name{mht.control}
\alias{mht.control}
\title{Controls for Manhattan plot}
\usage{
mht.control(
  type = "p",
  usepos = FALSE,
  logscale = TRUE,
  base = 10,
  cutoffs = NULL,
  colors = NULL,
  labels = NULL,
  gap = NULL,
  cex = 0.4,
  lab.cex = 1,
  axis.cex = 1.2,
  axis.lwd = 1.2,
  axis.tck = -0.02,
  yline = 3,
  xline = 3,
  verbose = FALSE
)
}
\arguments{
\item{type}{Character. Either \code{"p"} (points) or \code{"l"} (lines).}

\item{usepos}{Logical. Use real chromosomal positions instead of ordinal
marker order.}

\item{logscale}{Logical. If \code{TRUE}, values are transformed using
\code{-log(base)(value)} before plotting.}

\item{base}{Numeric. Base of logarithm used when \code{logscale = TRUE}.}

\item{cutoffs}{Numeric vector of horizontal reference lines to draw.}

\item{colors}{Vector of chromosome colours. Recycled as needed.}

\item{labels}{Optional chromosome labels for the x-axis.}

\item{gap}{Numeric. Gap inserted between chromosomes on the x-axis.}

\item{cex}{Numeric. Scaling factor for plotted points.}

\item{lab.cex}{Numeric. Scaling factor for chromosome labels on the x-axis.}

\item{axis.cex}{Numeric. Scaling factor for axis tick labels.
Increase when exporting high-resolution figures.}

\item{axis.lwd}{Numeric. Line width for axes and tick marks.}

\item{axis.tck}{Numeric. Length and direction of tick marks.
Negative values draw ticks outward (recommended for publication plots).}

\item{yline}{Numeric. Margin line for the y-axis label.}

\item{xline}{Numeric. Margin line for the x-axis label.}

\item{verbose}{Logical. Print plotting progress messages.}
}
\value{
a named list of control parameters for \code{\link[=mhtplot]{mhtplot()}}.
}
\description{
Parameter specification helper for \code{\link[=mhtplot]{mhtplot()}}. This function creates a list
of graphical and behavioural settings used when generating Manhattan plots.
}
\examples{
mht.control()
}
\seealso{
\code{\link[=mhtplot]{mhtplot()}}, \code{\link[=hmht.control]{hmht.control()}}
}
