plotQTL: Plot the results of a previous QTL analysis
In polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations

Description Usage Arguments Value Examples

Basic QTL plotting function, taking map positions and significance levels as input

plotQTL(
  LOD_data,
  support_interval = 0,
  ylimits = NULL,
  multiplot = NULL,
  plot_type = "lines",
  overlay = FALSE,
  add_xaxis = TRUE,
  add_rug = TRUE,
  mainTitle = FALSE,
  log = NULL,
  ...
)

`LOD_data`	Output list from `QTLscan` with items QTL.res and Perm.res (the latter can be `NULL`)
`support_interval`	Numeric. If 0 (by default) then there is no support interval returned. If greater than zero, then a LOD support interval is shown on output plot and the bounds are returned.
`ylimits`	Use to specify ylimits of plot region, though by default `NULL` in which case a suitable plot region is automatically used.
`multiplot`	Vector of integers. By default `NULL`. If `LOD_data` contains results from multiple linkage groups, you can define the number of rows and columns in the plot layout.
`plot_type`	How should be plots be drawn, either "lines" or "points" are possible
`overlay`	Add to an existing plot (should be produced by a comparable call to this function) or not? By default `FALSE`, in which case a new plot is drawn. Can be useful for displaying results of multiple analyses together.
`add_xaxis`	Should an x-axis be drawn? If multiple QTL analyses are performed on different traits, specifying this to be `FALSE` and using `par(mar=c(0,4.1,4.1,2.1))` allows subsequent plots to be neatly stacked.
`add_rug`	Logical, by default `TRUE` - should original marker points be added to plot?
`mainTitle`	Vector of plot titles (single character vector also allowed and will be recycled). For no plot titles, leave as `FALSE`
`log`	Character string specifying the log filename to which standard output should be written. If `NULL` log is send to stdout.
`...`	Extra arguments passed to plotting functions (plot, lines / points)