quantsmooth (version 1.38.0)

grid.chromosome: Draw a chromosome using the grid package

Description

A chromosme is drawn including the cytobands

Usage

grid.chromosome(chrom, side = 1, units = "hg19", 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 or data.frame, type of units for genomic data, or a dataframe with UCSC cytoband data, see lengthChromosome

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

Value

This function is executed for its side effects

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.

References

lodplot package

See Also

paintCytobands

Examples

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