mht.control: Controls for Manhattan plot
In gap: Genetic Analysis Package

mht.control

R Documentation

Controls for Manhattan plot

Description

Parameter specification helper for mhtplot(). This function creates a list of graphical and behavioural settings used when generating Manhattan plots.

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

`type`	Character. Either `"p"` (points) or `"l"` (lines).
`usepos`	Logical. Use real chromosomal positions instead of ordinal marker order.
`logscale`	Logical. If `TRUE`, values are transformed using `-log(base)(value)` before plotting.
`base`	Numeric. Base of logarithm used when `logscale = TRUE`.
`cutoffs`	Numeric vector of horizontal reference lines to draw.
`colors`	Vector of chromosome colours. Recycled as needed.
`labels`	Optional chromosome labels for the x-axis.
`gap`	Numeric. Gap inserted between chromosomes on the x-axis.
`cex`	Numeric. Scaling factor for plotted points.
`lab.cex`	Numeric. Scaling factor for chromosome labels on the x-axis.
`axis.cex`	Numeric. Scaling factor for axis tick labels. Increase when exporting high-resolution figures.
`axis.lwd`	Numeric. Line width for axes and tick marks.
`axis.tck`	Numeric. Length and direction of tick marks. Negative values draw ticks outward (recommended for publication plots).
`yline`	Numeric. Margin line for the y-axis label.
`xline`	Numeric. Margin line for the x-axis label.
`verbose`	Logical. Print plotting progress messages.