prepareGenomePlot {quantsmooth} | R Documentation |
This function starts up a plot consisting of all chromosomes of a genomen, including axes with chromosome names.
prepareGenomePlot(chrompos, cols = "grey50", paintCytobands = FALSE, bleach = 0, topspace = 1, organism, sexChromosomes = FALSE, ...)
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 |
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.
A matrix with 2 columns that contain the Y and X positions for the probes on the plot
Jan Oosting