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

      if(match("hgu95av2.db", .packages(all = TRUE), nomatch=0)) {
        library("hgu95av2.db")
        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.db data package for the example")

[Package geneplotter version 1.20.0 Index]