grid.chromosome {quantsmooth}R Documentation

Draw a chromosome using the grid package

Description

A chromosme is drawn including the cytobands

Usage

grid.chromosome(chrom, side = 1, units = c("cM", "bases", "ISCN"), chrom.width = 0.5, length.out, 
             bands = "major", legend = c("chrom", "band", "none"), cex.leg = 0.7, bleach = 0, ...)

Arguments

chrom numeric or character, id of chromosome to plot
side numeric [1:4], side of rectangle to draw, 4 sides, side 2 and 4 are vertical
units character, type of unit to use
chrom.width numeric [0,1], The width relative to the width (sides 2 and 4) or height(sides 1 and 3) of the viewport
length.out numeric, size of native units of viewport
bands character, draw either major or minor bands
legend character, type of legend
cex.leg numeric, relative size of legend text
bleach numeric [0,1], proportion by which to bleach the chromosome
... arguments for viewport(), especially x,y, width, and height

Details

The chromosome is drawn within a rectangle defined by x, y, width, and height, which is pushed as a viewport. The legend is drawn within the same rectangle in the space left over by chrom.width.

Value

This function is executed for its side effects

Author(s)

David L Duffy ,Jan Oosting

References

lodplot package

See Also

paintCytobands

Examples

    
    grid.newpage()
    grid.chromosome(1,units="bases",height=0.15)


[Package quantsmooth version 1.8.0 Index]