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 1.5.4 Index]