synbreed (version 0.9-4)

plotGenMap: Plot marker map

Description

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

Usage

## S3 method for class 'GenMap':
plot(x, dense = FALSE, nMarker = TRUE, bw=1, centr=NULL, file=NULL, fileFormat="pdf",...)

plotGenMap(map, dense = FALSE, nMarker = TRUE, bw=1, centr=NULL, file=NULL, fileFormat="pdf",...)

Arguments

x

object of class GenMap, i. e. the map object in a gpData-object

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?

bw

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.

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".

...

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.

See Also

create.gpData

Examples

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

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