cColor {geneplotter}R Documentation

A function for marking specific probes on a cPlot.

Description

Given a set of probes, will highlight them in the color desired on a plot which has already been created via the function cPlot().

Usage

cColor(probes, color, plotChroms, scale=c("relative","max"),glen=0.4)

Arguments

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

Details

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().

Author(s)

Jeff Gentry

See Also

cPlot, chromLocation-class

Examples

   ## 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")

[Package geneplotter version 1.8.0 Index]