prepareGenomePlot {quantsmooth}R Documentation

Set up a full genome plot

Description

This function starts up a plot consisting of all chromosomes of a genomen, including axes with chromosome names.

Usage

prepareGenomePlot(chrompos, cols = "grey50", paintCytobands = FALSE, bleach = 0, topspace = 1, organism, sexChromosomes = FALSE, ...)

Arguments

chrompos chrompos object, data.frame with CHR column identifying the chromosome of probes, and a MapInfo column identifying the position on the chromosome
cols color(s) for the chromosome lines
paintCytobands logical, use paintCytoband to plot ideograms for all chromosomes
bleach numeric [0,1], proportion by which to bleach the ideograms
topspace numerical, extra space on top of plot, i.e. for legends
organism character, if given a 2 column plot is created with the chromosomes for the given species. Currently "hsa", "mmu", and "rno" are supported
sexChromosomes logical, if TRUE then also the sex chromosomes X and Y are plotted
... extra arguments for plot function

Details

If organism is not supplied then a single column is plotted of the available chromosomes in chrompos$CHR. The arguments paintCytobands, bleach, and sexChromosomes are not used in that case.

Value

A matrix with 2 columns that contain the Y and X positions for the probes on the plot

Author(s)

Jan Oosting


[Package quantsmooth version 1.8.0 Index]