cPlot {geneplotter} | R Documentation |
Given a chromLocation object, will plot all the gene locations from that object.
cPlot(plotChroms, useChroms=chromNames(plotChroms), scale=c("relative","max"), fg="white", bg="lightgrey", glen=0.4)
plotChroms |
An object of type chromLocation which contains all the gene information to be plotted. |
useChroms |
A vector of chromosome names to be used in the plot. Default is to use all the chromosomes from the plotChroms object. |
scale |
Passed on to cScale as it's scale argument. Determines whether the graph is scaled on a relative or absolute basis. |
fg |
The colour to be used for the genes. Default is white. |
bg |
The colour to be used for the background of the plot. Defaults to lightgrey/ |
glen |
A scaling factor applied to the plotted length of each gene. Defaults to 0.4 - it is recommended that this not be set larger then 0.5 as it will cause overlap between chromosomes. |
This function will first use the lengths of the chromosomes, stored in
the object to create scaling factors for the X axis. Once the
scaling factors are determined, the chromLocation
object which is
passed in is used to determine all the gene locations/strand
information/etc, which is then plotted for the user.
Jeff Gentry
cScale
, cColor
,
chromLocation-class
## A bit of a hack to not have a package dependency on hgu95av2 ## but need to fiddle w/ the warn level to not fail the example anyways. curWarn <- options(warn=0) on.exit(options(warn=curWarn), add=TRUE) if (require(hgu95av2)) { z <- buildChromLocation("hgu95av2") if (interactive()) { par(ask=TRUE) } for (sc in c("max","relative")) cPlot(z,c("1","5","10","X","Y"),sc) } else print("This example can not be run without hgu95av2 data package")