plotGenMap: Plot marker map

Description

A function to visualize low and high-density marker maps.

Usage

plotGenMap(map, dense = FALSE, nMarker = TRUE, bw=1, centr=NULL,...)

Arguments

map

object of class gpData with object map or a data.frame with columns 'chr' (specifying the chromosome of the marker) and 'pos' (position of the marker within chromosome measured with genetic or physical distances)

dense

logical. Should density visualization for high-density genetic maps be used?

nMarker

logical. Print number of markers for each chromosome?

numeric. Bandwidth to use for dense=TRUE to control the resolution (default = 1 [map unit]).

centr

numeric vector. Positions for the centromeres in the same order as chromosomes in map. If "maize", centromere positions of maize in Mbp are used.

...

further graphical arguments for function plot

Value

Plot of the marker positions within each chromosome. One chromosome is displayed from the first to the last marker.

Details

In the low density plot, the unique positions of markers are plotted as horizontal lines. In the high-density plot, the distribution of the markers is visualized as a heatmap of density estimation together with a color key. In this case, the number of markers within an interval of equal bandwidth bw is counted. The high density plot is typically useful if the number of markers exceeds 200 per chromosome on average.

Examples

Run this code

# low density plot
data(maize)
plotGenMap(maize)

# high density plot  
data(mice)
plotGenMap(mice,dense=TRUE,nMarker=FALSE)