grid.chromosome: Draw a chromosome using the grid package

In quantsmooth: Quantile smoothing and genomic visualization of array data

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

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)

quantsmooth documentation built on Nov. 8, 2020, 8:27 p.m.