Usage
# S3 method for LDdf
plot(x, gpData, plotType = "dist", dense = FALSE, nMarker = TRUE,
centr = NULL, chr = NULL, type = "p",breaks = NULL, n = NULL,
file = NULL, fileFormat = "pdf", onefile = TRUE, colL = 2,
colD = 1, ...)Arguments
x
Object of class LDdf, i.e the output of function pairwiseLD with argument type="data.frame".
gpData
Object of class gpData with object map
plotType
You can decide, if you like to have a plot with the LD of the neighbouring markers (option "neighbour"), or you like to have a scatter plot of distance and LD (default option "dist").
dense
For plotType="neighbour", logical. Should density visualization for high-density genetic maps be used?
nMarker
For plotType="neighbour", logical. Print number of markers for each chromosome?
centr
For plotType="neighbour", numeric vector. Positions for the centromeres in the same order as chromosomes in map. If "maize", centromere positions of maize in Mbp are used.
chr
For plotType="dist", numeric scalar or vector. Return value is a plot for each chromosome in chr. Note: Remember to add in a batch-script one empty line for each chromosome, if you use more than one chromosome!
type
For plotType="dist", character string to specify the type of plot. Use "p" for a scatterplot, "bars" for stacked bars or "nls" for scatterplot together with nonlinear regression curve according to Hill and Weir (1988).
breaks
For plotType="dist", list containing breaks for stacked bars (optional, only for type="bars"). Components are dist with breaks for distance on x-axis and r2 for breaks on for r2 on y-axis. By default, 5 equal spaced categories for dist and r2 are used.
n
For plotType="dist", numeric. Number of observations used to estimate LD. Only required for type="nls".
file
Optionally a path to a file where the plot is saved to
fileFormat
character. At the moment two file formats are supported: pdf and png. Default is "pdf".
onefile
logical. If fileFormat = "pdf" you can decide, if you like to have all graphics in one file or in multiple files.
colL
The color for the line if type="nls" is used. In other cases without a meaning.
colD
The color for the dots in the plot of type="nls" and type="p"
…
further graphical arguments for function plot