prepareGenomePlot: 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, units = "hg19",...)

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

units

characterr or data.frame, type of units for genomic data, or a dataframe with UCSC cytoband data, see lengthChromosome

...

extra arguments for plot function

Value

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

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. If organism is supplied and chrompos is NULL then a result is generated with the starting Y and X position of each chromosome