cColor {geneplotter} | R Documentation |
Given a set of probes, will highlight them in the color desired on a plot which has already been created via the function cPlot().
cColor(probes, color, plotChroms, scale=c("relative","max"),glen=0.4)
probes |
The probes that are being highlighted. |
color |
The color to highlight the probes. |
plotChroms |
An object of type chromLocation which contains all
the gene information to be plotted. |
scale |
Whether to plot the graph scaled absolutely or relative by chromosome. Default is absolute. |
glen |
The length of the gene line plotted |
It is important to call the function cPlot()
first. This function
will then search for the specific locations of the probes desired,
which are contained within the plotChroms
instance of a
chromLocation
class. It will then pass these on to the
plotting routine to highlight the desired locations. NOTE: It
is important that plotChroms
, scale
and glen
parameters are the same as used for cPlot()
.
Jeff Gentry
## 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") cPlot(z) probes <- c("266_s_at", "31411_at", "610_at", "failExample") cColor(probes, "red", z) probes2 <- c("960_g_at", "41807_at", "931_at", "39032_at") cColor(probes2, "blue", z) } else print("Need hgu95av2 data package to run example")