cPlot {geneplotter} | R Documentation

## A plotting function for chromosomes.

### Description

Given a chromLocation object, will plot all the gene locations from that object.

### Usage

    cPlot(plotChroms, useChroms=chromNames(plotChroms),
          scale=c("relative","max"), fg="white", bg="lightgrey",
          glen=0.4, xlab="", ylab="Chromosome",
          main = organism(plotChroms), ...)

### Arguments

`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.
`xlab` | A label for the x axis.
`ylab` | A label for the y axis.
`main` | A main label for the plot.
`...` | Additional graphics arguments, passed to `segments`, which is used to draw the vertical ticks.

### Details

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.

### Author(s)

Jeff Gentry

### See Also

`cScale`, `cColor`, `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(curWarn), add=TRUE)
       if (require("hgu95av2.db")) {
           z <- buildChromLocation("hgu95av2")

           if (interactive()) {
               curPar <- par(ask=TRUE)
               on.exit(par(curPar), add=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")

[Package geneplotter version 1.66.0 Index]